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Journal articles on the topic 'Transcriptome size'

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Author: Grafiati
Published: 7 July 2024

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1

Mora-Márquez, Fernando, José Luis Vázquez-Poletti, Víctor Chano, Carmen Collada, Álvaro Soto, and Unai López de Heredia. "Hardware Performance Evaluation of De novo Transcriptome Assembly Software in Amazon Elastic Compute Cloud." Current Bioinformatics 15, no. 5 (October 14, 2020): 420–30. http://dx.doi.org/10.2174/1574893615666191219095817.

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Background: Bioinformatics software for RNA-seq analysis has a high computational requirement in terms of the number of CPUs, RAM size, and processor characteristics. Specifically, de novo transcriptome assembly demands large computational infrastructure due to the massive data size, and complexity of the algorithms employed. Comparative studies on the quality of the transcriptome yielded by de novo assemblers have been previously published, lacking, however, a hardware efficiency-oriented approach to help select the assembly hardware platform in a cost-efficient way. Objective: We tested the performance of two popular de novo transcriptome assemblers, Trinity and SOAPdenovo-Trans (SDNT), in terms of cost-efficiency and quality to assess limitations, and provided troubleshooting and guidelines to run transcriptome assemblies efficiently. Methods: We built virtual machines with different hardware characteristics (CPU number, RAM size) in the Amazon Elastic Compute Cloud of the Amazon Web Services. Using simulated and real data sets, we measured the elapsed time, cost, CPU percentage and output size of small and large data set assemblies. Results: For small data sets, SDNT outperformed Trinity by an order the magnitude, significantly reducing the time duration and costs of the assembly. For large data sets, Trinity performed better than SDNT. Both the assemblers provide good quality transcriptomes. Conclusion: The selection of the optimal transcriptome assembler and provision of computational resources depend on the combined effect of size and complexity of RNA-seq experiments.
2

Ikeda, Hiroki, Shintaro Miyao, So Nagaoka, Tomoya Takashima, Sze-Ming Law, Takuya Yamamoto, and Kazuki Kurimoto. "High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis." Life Science Alliance 6, no. 11 (September 18, 2023): e202301929. http://dx.doi.org/10.26508/lsa.202301929.

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High-quality, straightforward single-cell RNA sequencing (RNA-seq) with spatial resolution remains challenging. Here, we developed DRaqL (direct RNA recovery and quenching for laser capture microdissection), an experimental approach for efficient cell lysis of tissue sections, directly applicable to cDNA amplification. Single-cell RNA-seq combined with DRaqL allowed transcriptomic profiling from alcohol-fixed sections with efficiency comparable with that of profiling from freshly dissociated cells, together with effective exon–exon junction profiling. The combination of DRaqL with protease treatment enabled robust and efficient single-cell transcriptome analysis from formalin-fixed tissue sections. Applying this method to mouse ovarian sections, we were able to predict the transcriptome of oocytes by their size and identified an anomaly in the size–transcriptome relationship relevant to growth retardation of oocytes, in addition to detecting oocyte-specific splice isoforms. Furthermore, we identified differentially expressed genes in granulosa cells in association with their proximity to the oocytes, suggesting distinct epigenetic regulations and cell-cycle activities governing the germ–soma relationship. Thus, DRaqL is a versatile, efficient approach for high-quality single-cell RNA-seq from tissue sections, thereby revealing histological heterogeneity in folliculogenic transcriptome.
3

Gonzalez-Ibeas, Daniel, Pedro J. Martinez-Garcia, Randi A. Famula, Annette Delfino-Mix, Kristian A. Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, and Jill L. Wegrzyn. "Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)." G3 Genes|Genomes|Genetics 6, no. 12 (December 1, 2016): 3787–802. http://dx.doi.org/10.1534/g3.116.032805.

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Abstract Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
4

Stern, M. D., S. V. Anisimov, and K. R. Boheler. "Can transcriptome size be estimated from SAGE catalogs?" Bioinformatics 19, no. 4 (March 1, 2003): 443–48. http://dx.doi.org/10.1093/bioinformatics/btg018.

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Beisser, Daniela, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, and Jens Boenigk. "Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes." PeerJ 5 (January 10, 2017): e2832. http://dx.doi.org/10.7717/peerj.2832.

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BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (December 28, 2017): 16. http://dx.doi.org/10.12688/gatesopenres.12783.1.

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Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised the single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 transcripts across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels between 54.1-75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
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Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (February 13, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.2.

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Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
8

Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition." Gates Open Research 1 (March 8, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.3.

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Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
9

Caurcel, Carlos, Dominik R. Laetsch, Richard Challis, Sujai Kumar, Karim Gharbi, and Mark Blaxter. "MolluscDB: a genome and transcriptome database for molluscs." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1825 (April 5, 2021): 20200157. http://dx.doi.org/10.1098/rstb.2020.0157.

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As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
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Jensen, Michael Krogh, Josef Korbinian Vogt, Simon Bressendorff, Andaine Seguin-Orlando, Morten Petersen, Thomas Sicheritz-Pontén, and John Mundy. "Transcriptome and Genome Size Analysis of the Venus Flytrap." PLOS ONE 10, no. 4 (April 17, 2015): e0123887. http://dx.doi.org/10.1371/journal.pone.0123887.

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Coate, Jeremy E., and Jeff J. Doyle. "Variation in transcriptome size: are we getting the message?" Chromosoma 124, no. 1 (November 26, 2014): 27–43. http://dx.doi.org/10.1007/s00412-014-0496-3.

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Ortiz, Randy, Priyanka Gera, Christopher Rivera, and Juan C. Santos. "Pincho: A Modular Approach to High Quality De Novo Transcriptomics." Genes 12, no. 7 (June 22, 2021): 953. http://dx.doi.org/10.3390/genes12070953.

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Transcriptomic reconstructions without reference (i.e., de novo) are common for data samples derived from non-model biological systems. These assemblies involve massive parallel short read sequence reconstructions from experiments, but they usually employ ad-hoc bioinformatic workflows that exhibit limited standardization and customization. The increasing number of transcriptome assembly software continues to provide little room for standardization which is exacerbated by the lack of studies on modularity that compare the effects of assembler synergy. We developed a customizable management workflow for de novo transcriptomics that includes modular units for short read cleaning, assembly, validation, annotation, and expression analysis by connecting twenty-five individual bioinformatic tools. With our software tool, we were able to compare the assessment scores based on 129 distinct single-, bi- and tri-assembler combinations with diverse k-mer size selections. Our results demonstrate a drastic increase in the quality of transcriptome assemblies with bi- and tri- assembler combinations. We aim for our software to improve de novo transcriptome reconstructions for the ever-growing landscape of RNA-seq data derived from non-model systems. We offer guidance to ensure the most complete transcriptomic reconstructions via the inclusion of modular multi-assembly software controlled from a single master console.
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Gross, Joshua B., Dennis A. Sun, Brian M. Carlson, Sivan Brodo-Abo, and Meredith E. Protas. "Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus." Genes 11, no. 1 (December 29, 2019): 42. http://dx.doi.org/10.3390/genes11010042.

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Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.
14

Nomburg, Jason, Wei Zou, Thomas C. Frost, Chandreyee Datta, Shobha Vasudevan, Gabriel J. Starrett, Michael J. Imperiale, Matthew Meyerson, and James A. DeCaprio. "Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses." PLOS Pathogens 18, no. 4 (April 1, 2022): e1010401. http://dx.doi.org/10.1371/journal.ppat.1010401.

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Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families.
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Ahn, Taejin, Kidong Kim, Hyojin Kim, Sarah Kim, Sangick Park, and Kyoungbun Lee. "A transcriptome-Based Deep Neural Network Classifier for Identifying the Site of Origin in Mucinous Cancer." Cancer Informatics 21 (January 2022): 117693512211351. http://dx.doi.org/10.1177/11769351221135141.

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Purpose: There is a lack of tools for identifying the site of origin in mucinous cancer. This study aimed to evaluate the performance of a transcriptome-based classifier for identifying the site of origin in mucinous cancer. Materials And Methods: Transcriptomic data of 1878 non-mucinous and 82 mucinous cancer specimens, with 7 sites of origin, namely, the uterine cervix (CESC), colon (COAD), pancreas (PAAD), stomach (STAD), uterine endometrium (UCEC), uterine carcinosarcoma (UCS), and ovary (OV), obtained from The Cancer Genome Atlas, were used as the training and validation sets, respectively. Transcriptomic data of 14 mucinous cancer specimens from a tissue archive were used as the test set. For identifying the site of origin, a set of 100 differentially expressed genes for each site of origin was selected. After removing multiple iterations of the same gene, 427 genes were chosen, and their RNA expression profiles, at each site of origin, were used to train the deep neural network classifier. The performance of the classifier was estimated using the training, validation, and test sets. Results: The accuracy of the model in the training set was 0.998, while that in the validation set was 0.939 (77/82). In the test set which is newly sequenced from a tissue archive, the model showed an accuracy of 0.857 (12/14). t-SNE analysis revealed that samples in the test set were part of the clusters obtained for the training set. Conclusion: Although limited by small sample size, we showed that a transcriptome-based classifier could correctly identify the site of origin of mucinous cancer.
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Haroon, Yu-Xin Li, Chen-Xu Ye, Jian Su, Ghulam Nabi, Xiao-Hong Su, and Lian-Xi Xing. "De Novo Transcriptome Assembly and Analysis of Longevity Genes Using Subterranean Termite (Reticulitermes chinensis) Castes." International Journal of Molecular Sciences 23, no. 21 (November 7, 2022): 13660. http://dx.doi.org/10.3390/ijms232113660.

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The longevity phenomenon is entirely controlled by the insulin signaling pathway (IIS-pathway). Both vertebrates and invertebrates have IIS-pathways that are comparable to one another, though no one has previously described de novo transcriptome assembly of IIS-pathway-associated genes in termites. In this research, we analyzed the transcriptomes of both reproductive (primary kings “PK” and queens “PQ”, secondary worker reproductive kings “SWRK” and queens “SWRQ”) and non-reproductive (male “WM” and female “WF” workers) castes of the subterranean termite Reticulitermes chinensis. The goal was to identify the genes responsible for longevity in the reproductive and non-reproductive castes. Through transcriptome analysis, we annotated 103,589,264 sequence reads and 184,436 (7G) unigenes were assembled, GC performance was measured at 43.02%, and 64,046 sequences were reported as CDs sequences. Of which 35 IIS-pathway-associated genes were identified, among 35 genes, we focused on the phosphoinositide-dependent kinase-1 (Pdk1), protein kinase B2 (akt2-a), tuberous sclerosis-2 (Tsc2), mammalian target of rapamycin (mTOR), eukaryotic translation initiation factor 4E (EIF4E) and ribosomal protein S6 (RPS6) genes. Previously these genes (Pdk1, akt2-a, mTOR, EIF4E, and RPS6) were investigated in various organisms, that regulate physiological effects, growth factors, protein translation, cell survival, proliferation, protein synthesis, cell metabolism and survival, autophagy, fecundity rate, egg size, and follicle number, although the critical reason for longevity is still unclear in the termite castes. However, based on transcriptome profiling, the IIS-pathway-associated genes could prolong the reproductive caste lifespan and health span. Therefore, the transcriptomic shreds of evidence related to IIS-pathway genes provide new insights into the maintenance and relationships between biomolecular homeostasis and remarkable longevity. Finally, we propose a strategy for future research to decrypt the hidden costs associated with termite aging in reproductive and non-reproductive castes.
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Lin, Xinghua, Dayan Zhou, Xiaomin Zhang, Guangli Li, Yulei Zhang, Cailin Huang, Zhixin Zhang, and Changxu Tian. "A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus)." Animals 11, no. 4 (April 15, 2021): 1131. http://dx.doi.org/10.3390/ani11041131.

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Hong Kong catfish (Clarias fuscus) exhibit sexual dimorphism, particularly in body size. Due to the fast growth rate of males, the sexual size dimorphism of Hong Kong catfish has become an economically important trait. However, limited knowledge is known about the molecular mechanisms of sex determination and sex differentiation in this species. In this study, a first de novo transcriptome sequencing analysis of testes and ovaries was performed to identify sex-biased genes in Hong Kong catfish. The results showed that a total of 290,291 circular consensus sequences (CCSs) were obtained, from which 248,408 full-length non-chimeric (FLNC) reads were generated. After non-redundant analysis, a total of 37,305 unigenes were predicted, in which 34,342 unigenes were annotated with multiple public databases. Comparative transcriptomic analysis identified 5750 testis-biased differentially expressed genes (DEGs) and 6991 ovary-biased DEGs. The enrichment analysis showed that DEGs were classified into 783 Gene Ontology (GO) terms and 16 Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. Many DEGs were involved with sex-related GO terms and KEGG pathways, such as oocyte maturation, androgen secretion, gonadal development and steroid biosynthesis pathways. In addition, the expression levels of 23 unigenes were confirmed to validate the transcriptomic data by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first investigation into the transcriptome of Hong Kong catfish testes and ovaries. This study provides an important molecular basis for the sex determination and sex control breeding of Hong Kong catfish.
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Garner, Terence, Philip Murray, Andrew James Whatmore, Peter Ellis Clayton, and Adam Stevens. "An Epigenomic Signature in Children Born Small for Gestational Age (SGA) With “Catch-up” Growth Is Present From Birth and Predicts Early Adulthood Pre-Hypertension." Journal of the Endocrine Society 5, Supplement_1 (May 1, 2021): A654—A655. http://dx.doi.org/10.1210/jendso/bvab048.1334.

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Abstract Background: Cardiometabolic conditions in adulthood are more common in children born SGA1. The relationship of the transcriptome (gene expression) and epigenome (DNA methylation) to birth size and the future development of cardiometabolic disease has not been characterized. Aims: To identify I) the relationship between epigenome at age 0, 7 and 17 years, transcriptome at age 9 years and birth size in a normal population; II) links between the transcriptome and epigenome in childhood and adult cardiometabolic risk. Study Design: Normal children (n=6487) from the Avon Longitudinal Study of Parents and Children were assigned to groups based on birth size using bodyweight (BW) and gestation and divided into groups using the population 10th centile. Adverse cardiometabolic risk at age 17 years was defined by the National Heart Lung and Blood Institute criteria of prehypertension using systolic and diastolic blood pressure as well as HDL and LDL2. Blood transcriptome at age 9 and blood epigenome at age 0, 7, and 17 years and were available from 980 and 947 children, respectively. Hypernetworks were used to integrate differentially expressed genes in the transcriptome (DEGs) and differentially methylated points (DMPs) in the epigenome, identifying functional links. Random Forest, a machine learning approach, was used to determine the predictive value of ‘omic data presented as the area under the curve (AUC) of the receiver operating characteristic. Results: Pre-hypertensive participants at age 17 years were distinguished from normotensive participants and this group was enriched for children born small who caught up by age 7 years (155/611 unhealthy/healthy SGA compared to 1979/12746 in all other BW groups; 1.6-fold, p<1x10-5). This group had a greater height velocity during their catch-up period than the normotensive participants (1.2-fold, p=0.027). Hypernetwork integration of ‘omic data identified a functional relationship between 55 DEGs at age 9 years and DMPs at age 7 years. Random forest analysis was able to accurately predict the presence of pre-hypertensive young adults from the age 9 transcriptome (AUC: 0.973). Using a gene-level contraction of DMPs which map to the 55 DEGs (i.e. cis-DMPs), we demonstrated accurate classification of pre-hypertensive young adults from their blood methylome at age 0 (AUC [95% CI]: 0.92 [0.89-0.95]), 7 (0.90 [0.87-0.93]), and 17 (0.91 [0.88-0.94]) years. Conclusions: Through the integration of transcriptome and epigenome, we have identified a set of genes with an epigenomic and transcriptomic signature which predict pre-hypertension in children born SGA who catch up. Specifically, we have shown that the associated epigenomic signature tracks from birth to early adulthood, indicating the possibility of early detection of risk and primordial prevention. 1 Barker etal. (1988) BMJ 297(6641):134-135. 2 Chobanian etal. (2003) JAMA 289(19):2560-2571.
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Coate, Jeremy E., and Jeff J. Doyle. "Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid." Genome Biology and Evolution 2 (January 1, 2010): 534–46. http://dx.doi.org/10.1093/gbe/evq038.

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Jiang, Wansheng, Yicheng Guo, Kunfeng Yang, Qiong Shi, and Junxing Yang. "Insights into Body Size Evolution: A Comparative Transcriptome Study on Three Species of Asian Sisoridae Catfish." International Journal of Molecular Sciences 20, no. 4 (February 21, 2019): 944. http://dx.doi.org/10.3390/ijms20040944.

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Body size is one of the most important attributes of a species, but the basic question of why and how each species reaches a different “right size” is still largely unknown. Herein, three phylogenetically closely related catfishes from Sisoridae, including one extraordinarily large-sized Bagarius yarrelli and two average-sized Glyptothorax macromaculatus and Oreoglanis setiger, were comparatively studied using RNA-Seq. Approximately 17,000 protein-coding genes were annotated for each of the three fishes, and 9509 genes were identified as high-confidence orthologous gene pairs. Comparative expressions uncovered a similar functional cluster about ribosome biogenesis was enriched in different tissues of the upregulated genes of Bagarius yarrelli. Moreover, differentially expressed genes and positively selected genes revealed that the glycolysis/pyruvate metabolism and cell cycle pathways have also greatly enhanced in this large-sized species. In total, 20 size-related candidate genes (including two growth modulators: the serine/threonine-protein kinases 3 (AKT3) and adaptor protein 1 (SH2B1), and a crucial pyruvate kinase (PKM2A)) were identified by multiplying comparative analyses along with gene functional screening, which would play major roles in enabling the large body size associated with Bagarius yarrelli and provide new insights into body size evolution. In conjunction with field observations and morphological comparisons, we hypothesize that habitat preferences promote size divergence of sisorids.
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Weirather, Jason L., Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, and Kin Fai Au. "Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis." F1000Research 6 (June 19, 2017): 100. http://dx.doi.org/10.12688/f1000research.10571.2.

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Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacBio and ONT, including error pattern, length, mappability and technical improvements over previous platforms. We also evaluated their application to transcriptome analyses, such as isoform identification and quantification and characterization of transcriptome complexity, by comparing the performance of size-selected PacBio, non-size-selected ONT and their corresponding Hybrid-Seq strategies (PacBio+Illumina and ONT+Illumina). Results: PacBio shows overall better data quality, while ONT provides a higher yield. As with data quality, PacBio performs marginally better than ONT in most aspects for both long reads only and Hybrid-Seq strategies in transcriptome analysis. In addition, Hybrid-Seq shows superior performance over long reads only in most transcriptome analyses. Conclusions: Both PacBio and ONT sequencing are suitable for full-length single-molecule transcriptome analysis. As this first use of ONT reads in a Hybrid-Seq analysis has shown, both PacBio and ONT can benefit from a combined Illumina strategy. The tools and analytical methods developed here provide a resource for future applications and evaluations of these rapidly-changing technologies.
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Gad, Ahmed, Lucie Nemcova, Matej Murin, Veronika Kinterova, Jiri Kanka, Jozef Laurincik, Michal Benc, Lazo Pendovski, and Radek Prochazka. "Global transcriptome analysis of porcine oocytes in correlation with follicle size." Molecular Reproduction and Development 87, no. 1 (November 17, 2019): 102–14. http://dx.doi.org/10.1002/mrd.23294.

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Chen, Chien-Chih, Wen-Dar Lin, Yu-Jung Chang, Chuen-Liang Chen, and Jan-Ming Ho. "Enhancing De Novo Transcriptome Assembly by Incorporating Multiple Overlap Sizes." ISRN Bioinformatics 2012 (April 23, 2012): 1–9. http://dx.doi.org/10.5402/2012/816402.

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Background. The emergence of next-generation sequencing platform gives rise to a new generation of assembly algorithms. Compared with the Sanger sequencing data, the next-generation sequence data present shorter reads, higher coverage depth, and different error profiles. These features bring new challenging issues for de novo transcriptome assembly. Methodology. To explore the influence of these features on assembly algorithms, we studied the relationship between read overlap size, coverage depth, and error rate using simulated data. According to the relationship, we propose a de novo transcriptome assembly procedure, called Euler-mix, and demonstrate its performance on a real transcriptome dataset of mice. The simulation tool and evaluation tool are freely available as open source. Significance. Euler-mix is a straightforward pipeline; it focuses on dealing with the variation of coverage depth of short reads dataset. The experiment result showed that Euler-mix improves the performance of de novo transcriptome assembly.
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Anisimov, Sergey V. "A Prevalence of Imprinted Genes within the Total Transcriptomes of Human Tissues and Cells." Molecular Biology International 2012 (September 11, 2012): 1–29. http://dx.doi.org/10.1155/2012/793506.

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Genomic imprinting is an epigenetic phenomenon that causes a differential expression of paternally and maternally inherited alleles of a subset of genes (the so-called imprinted genes). Imprinted genes are distributed throughout the genome and it is predicted that about 1% of the human genes may be imprinted. It is recognized that the allelic expression of imprinted genes varies between tissues and developmental stages. The current study represents the first attempt to estimate a prevalence of imprinted genes within the total human transcriptome. In silico analysis of the normalized expression profiles of a comprehensive panel of 173 established and candidate human imprinted genes was performed, in 492 publicly available SAGE libraries. The latter represent human cell and tissue samples in a variety of physiological and pathological conditions. Variations in the prevalence of imprinted genes within the total transcriptomes (ranging from 0.08% to 4.36%) and expression profiles of the individual imprinted genes are assessed. This paper thus provides a useful reference on the size of the imprinted transcriptome and expression of the individual imprinted genes.
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Kelly, Morgan W., Jacqueline L. Padilla-Gamiño, and Gretchen E. Hofmann. "High pCO2 affects body size, but not gene expression in larvae of the California mussel (Mytilus californianus)." ICES Journal of Marine Science 73, no. 3 (October 21, 2015): 962–69. http://dx.doi.org/10.1093/icesjms/fsv184.

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Abstract Many studies have reported reductions in body size and calcification rates for marine larvae exposed to ocean acidification conditions. However, the physiological mechanisms driving these effects, and mechanisms underlying body size variation in general, are poorly understood. Here, we combine transcriptome sequencing with bulked segregant analysis to assess the physiological response to acidification in larvae of the California mussel, Mytilus californianus, and to explore physiological basis of variation in larval size. We reared three families of M. californianus larvae under ambient (∼350 µatm, pHtotal 8.1) and high (∼1300 µatm, pHtotal 7.6) pCO2 conditions, then passed larvae through a mesh filter, separating each family × pCO2 treatment into fractions of larvae with large vs. small body sizes. We sequenced larval mRNA for each family × treatment × body size combination, and assembled a de novo transcriptome. We then mapped reads from each library to this assembly to identify effects of high pCO2 on gene expression, and to identify transcriptomic differences between small vs. large larvae of the same age class. Although larvae reared under elevated pCO2 were smaller, we observed no consistent effect of elevated pCO2 on gene expression. Nevertheless, 1225 transcripts, primarily related to metabolism, were differentially expressed between large vs. small larvae, regardless of CO2 treatment. We conclude that the observed reduction in larval body size under high CO2 may be driven by a direct effect of the environment on phenotype, unmediated by changes in gene expression. Because M. calfornianus has evolved in the context of seasonal upwelling, exposure to 1300 µatm, pCO2 may not produce the large stress-mediated effects on gene expression that might be expected for an organism exposed to conditions far outside those of its typical environment.
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Jin, Ai-Hua, Sébastien Dutertre, Mriga Dutt, Vincent Lavergne, Alun Jones, Richard Lewis, and Paul Alewood. "Transcriptomic-Proteomic Correlation in the Predation-Evoked Venom of the Cone Snail, Conus imperialis." Marine Drugs 17, no. 3 (March 19, 2019): 177. http://dx.doi.org/10.3390/md17030177.

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Individual variation in animal venom has been linked to geographical location, feeding habit, season, size, and gender. Uniquely, cone snails possess the remarkable ability to change venom composition in response to predatory or defensive stimuli. To date, correlations between the venom gland transcriptome and proteome within and between individual cone snails have not been reported. In this study, we use 454 pyrosequencing and mass spectrometry to decipher the transcriptomes and proteomes of the venom gland and corresponding predation-evoked venom of two specimens of Conus imperialis. Transcriptomic analyses revealed 17 conotoxin gene superfamilies common to both animals, including 5 novel superfamilies and two novel cysteine frameworks. While highly expressed transcripts were common to both specimens, variation of moderately and weakly expressed precursor sequences was surprisingly diverse, with one specimen expressing two unique gene superfamilies and consistently producing more paralogs within each conotoxin gene superfamily. Using a quantitative labelling method, conotoxin variability was compared quantitatively, with highly expressed peptides showing a strong correlation between transcription and translation, whereas peptides expressed at lower levels showed a poor correlation. These results suggest that major transcripts are subject to stabilizing selection, while minor transcripts are subject to diversifying selection.
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DeCaprio, James A., Jason Nomburg, and Matthew Meyerson. "Abstract SY11-02: Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses." Cancer Research 82, no. 12_Supplement (June 15, 2022): SY11–02—SY11–02. http://dx.doi.org/10.1158/1538-7445.am2022-sy11-02.

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Abstract Polyomaviruses (PyV) are ubiquitous pathogens that can cause devastating human diseases. Due to the small size of their genomes, PyV utilize complex patterns of RNA splicing to maximize their coding capacity. Despite the importance of PyV to human disease, their transcriptome architecture is poorly characterized. Here, we compare short- and long-read RNA sequencing data from eight human and non-human PyV. We provide a detailed transcriptome atlas for BK polyomavirus (BKPyV), an important human pathogen, and the prototype PyV, simian virus 40 (SV40). We identify pervasive wraparound transcription in PyV, wherein transcription runs through the polyA site and circles the genome multiple times. Comparative analyses identify novel, conserved transcripts that increase PyV coding capacity. One of these conserved transcripts encodes superT, a T antigen containing two RB-binding LxCxE motifs. We find that superT-encoding transcripts are abundant in PyV-associated human cancers. Together, we show that comparative transcriptomic approaches can greatly expand known transcript and coding capacity in one of the simplest and most well-studied viral families. Citation Format: James A. DeCaprio, Jason Nomburg, Matthew Meyerson. Long-read sequencing reveals complex patterns of wraparound transcription in polyomaviruses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr SY11-02.
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Zhang, Lei, Jiujun Du, Xiaolan Ge, Demei Cao, and Jianjun Hu. "Leaf Size Development Differences and Comparative Transcriptome Analyses of Two Poplar Genotypes." Genes 12, no. 11 (November 9, 2021): 1775. http://dx.doi.org/10.3390/genes12111775.

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The plant leaf, the main organ of photosynthesis, is an important regulator of growth. To explore the difference between leaf size of Populusdeltoides ‘Danhong’ (Pd) and Populus simonii ‘Tongliao1’ (Ps), we investigated the leaf length, leaf width, leaf thickness, leaf area, leaf mass per area (LMA), and cell size of leaves from two genotypes and profiled the transcriptome-wide gene expression patterns through RNA sequencing. Our results show that the leaf area of Pd was significantly larger than that of Ps, but the epidermal cell area was significantly smaller than that of Ps. The difference of leaf size was caused by cell numbers. Transcriptome analysis also revealed that genes related to chromosome replication and DNA repair were highly expressed in Pd, while genes such as the EXPANSIN (EXPA) family which promoted cell expansion were highly expressed in Ps. Further, we revealed that the growth-regulating factors (GRFs) played a key role in the difference of leaf size between two genotypes through regulation of cell proliferation. These data provide a valuable resource for understanding the leaf development of the Populus genus.
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Toh, Su, and Michael Perlin. "Size Does Matter: Staging of Silene latifolia Floral Buds for Transcriptome Studies." International Journal of Molecular Sciences 16, no. 9 (September 11, 2015): 22027–45. http://dx.doi.org/10.3390/ijms160922027.

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Kaisers, Wolfgang, Holger Schwender, and Heiner Schaal. "Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data." International Journal of Molecular Sciences 18, no. 9 (September 5, 2017): 1900. http://dx.doi.org/10.3390/ijms18091900.

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Pan, Xiao, Abdulaziz A. Alsayyari, Ciska Dalm, Jos A. Hageman, René H. Wijffels, and Dirk E. Martens. "Transcriptome Analysis of CHO Cell Size Increase During a Fed-Batch Process." Biotechnology Journal 14, no. 3 (July 30, 2018): 1800156. http://dx.doi.org/10.1002/biot.201800156.

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Shang, Huiying, Lulu Xun, Tao Miao, Chen Chen, Yuan Lu, and Bin Li. "Transcriptome Analysis Provides Valuable Insights into Leaf Size Variation in Rhamnus heterophylla." Agronomy 14, no. 2 (February 18, 2024): 396. http://dx.doi.org/10.3390/agronomy14020396.

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The size of leaves is a vital factor in the development and overall biomass of a plant, serving as a key indicator of how a plant adapts to its environment. Rhamnus heterophylla, a species known for its heteromorphic leaves of varying sizes, presents an intriguing case for studying leaf development at the molecular level. To gain insights for further studies on the underlying mechanisms, we constructed a comprehensive reference transcriptome database using both SMART sequencing and Illumina RNA-seq technologies. Our analysis of the transcriptome data identified 88,546 isoforms, featuring an N50 size of 2386 base pairs. Furthermore, we identified 2932 transcription factors from 55 gene families, along with 14,947 unigenes that underwent alternative splicing. By comparing the gene expression patterns between large and small leaves, we pinpointed 982 differentially expressed genes (DEGs). Among these DEGs, 116 genes exhibit significantly greater activity in small leaves, while 866 genes display significantly greater activity in large leaves. Functional enrichment analyses revealed the significant involvement of these DEGs in various hormone signaling pathways. Notably, we detected a significant decrease in the expression of several genes associated with auxin synthesis, such as ARFs, GRF8, and IAA27, in small leaves. This finding sheds light on their potential role in leaf size regulation in R. heterophylla, providing valuable insights into the genes underlying this mechanism.
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Son, Park, Jung, Singh, Lee, Kim, and Lee. "Integrated Metabolomics and Transcriptomics Unravel the Metabolic Pathway Variations for Different Sized Beech Mushrooms." International Journal of Molecular Sciences 20, no. 23 (November 28, 2019): 6007. http://dx.doi.org/10.3390/ijms20236007.

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Beech mushrooms (Hypsizygus marmoreus) are largely relished for their characteristic earthy flavor, chewy-texture, and gustatory and nutritional properties in East Asian societies. Intriguingly, the aforementioned properties of beech mushroom can be subsumed under its elusive metabolome and subtle transcriptome regulating its various stages of growth and development. Herein, we carried out an integrated metabolomic and transcriptomic profiling for different sized beech mushrooms across spatial components (cap and stipe) to delineate their signature pathways. We observed that metabolite profiles and differentially expressed gene (DEGs) displayed marked synergy for specific signature pathways according to mushroom sizes. Notably, the amino acid, nucleotide, and terpenoid metabolism-related metabolites and genes were more abundant in small-sized mushrooms. On the other hand, the relative levels of carbohydrates and TCA intermediate metabolites as well as corresponding genes were linearly increased with mushroom size. However, the composition of flavor-related metabolites was varying in different sized beech mushrooms. Our study explores the signature pathways associated with growth, development, nutritional, functional and organoleptic properties of different sized beech mushrooms.
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Zhang, Hongyuan, Jie Tan, Min Zhang, Shuping Huang, and Xia Chen. "Comparative Transcriptomic Analysis of Two Bottle Gourd Accessions Differing in Fruit Size." Genes 11, no. 4 (March 27, 2020): 359. http://dx.doi.org/10.3390/genes11040359.

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The bottle gourd (Lagenaria siceraria) is an important horticultural and medicinal crop with high nutritional value. This study aimed at examining the molecular regulation of fruit size in bottle gourd. We performed transcriptome sequencing of two bottle gourd cultivars differing in their fruit size. The average fruit length and weight of the cultivar Hang (39.48 cm/624.4 g) were higher than those of the cultivar USA (10.34 cm/152.8 g) at maturity. Transcriptome sequencing and assembly resulted in 89,347 unigenes. A total of 1250 differentially expressed genes (DEG) were found between the two cultivars, including 422 upregulated genes and 828 downregulated genes in Hang as compared to USA. Genes related to cell wall metabolism, phytohormones, cell cycle, and cell division showed significant differential expression between the two cultivars. DEGs encoding transcription factors (TF) from nine TF families were also identified. The ethylene response factor family was the most enriched among these families. Our study provides a basis for further investigations of the molecular regulation of fruit size in bottle gourd.
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Saker, Halima, Rainer Machné, Jörg Fallmann, Douglas B. Murray, Ahmad M. Shahin, and Peter F. Stadler. "Weighted Consensus Segmentations." Computation 9, no. 2 (February 5, 2021): 17. http://dx.doi.org/10.3390/computation9020017.

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The problem of segmenting linearly ordered data is frequently encountered in time-series analysis, computational biology, and natural language processing. Segmentations obtained independently from replicate data sets or from the same data with different methods or parameter settings pose the problem of computing an aggregate or consensus segmentation. This Segmentation Aggregation problem amounts to finding a segmentation that minimizes the sum of distances to the input segmentations. It is again a segmentation problem and can be solved by dynamic programming. The aim of this contribution is (1) to gain a better mathematical understanding of the Segmentation Aggregation problem and its solutions and (2) to demonstrate that consensus segmentations have useful applications. Extending previously known results we show that for a large class of distance functions only breakpoints present in at least one input segmentation appear in the consensus segmentation. Furthermore, we derive a bound on the size of consensus segments. As show-case applications, we investigate a yeast transcriptome and show that consensus segments provide a robust means of identifying transcriptomic units. This approach is particularly suited for dense transcriptomes with polycistronic transcripts, operons, or a lack of separation between transcripts. As a second application, we demonstrate that consensus segmentations can be used to robustly identify growth regimes from sets of replicate growth curves.
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Li, Huawei, Yujing Suo, Hui Li, Peng Sun, Shuzhan Li, Deyi Yuan, Weijuan Han, and Jianmin Fu. "Cytological and Transcriptome Analyses Provide Insights into Persimmon Fruit Size Formation (Diospyros kaki Thunb.)." International Journal of Molecular Sciences 25, no. 13 (June 30, 2024): 7238. http://dx.doi.org/10.3390/ijms25137238.

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Persimmon (Diospyros kaki Thunb.) fruit size variation is abundant. Studying the size of the persimmon fruit is helpful in improving its economic value. At present, the regulatory mechanism of persimmon fruit size formation is still unclear. In this study, the mechanism of fruit size formation was investigated through morphological, cytological and transcriptomic analyses, as well as exogenous ethrel and aminoethoxyinylglycine (AVG: ethylene inhibitor) experiments using the large fruit and small fruit of ‘Yaoxianwuhua’. The results showed that stages 3–4 (June 11–June 25) are the crucial morphological period for differentiation of large fruit and small fruit in persimmon. At this crucial morphological period, the cell number in large fruit was significantly more than that in small fruit, indicating that the difference in cell number is the main reason for the differentiation of persimmon fruit size. The difference in cell number was caused by cell division. CNR1, ANT, LAC17 and EB1C, associated with cell division, may be involved in regulating persimmon fruit size. Exogenous ethrel resulted in a decrease in fruit weight, and AVG treatment had the opposite effect. In addition, LAC17 and ERF114 were upregulated after ethrel treatment. These results indicated that high ethylene levels can reduce persimmon fruit size, possibly by inhibiting cell division. This study provides valuable information for understanding the regulation mechanism of persimmon fruit size and lays a foundation for subsequent breeding and artificial regulation of fruit size.
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Fischer, Sarah, Nicolas Spath, and Mohamed Hamed. "Data-Driven Radiogenomic Approach for Deciphering Molecular Mechanisms Underlying Imaging Phenotypes in Lung Adenocarcinoma: A Pilot Study." International Journal of Molecular Sciences 24, no. 5 (March 3, 2023): 4947. http://dx.doi.org/10.3390/ijms24054947.

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The heterogeneity of lung tumor nodules is reflected in their phenotypic characteristics in radiological images. The radiogenomics field employs quantitative image features combined with transcriptome expression levels to understand tumor heterogeneity molecularly. Due to the different data acquisition techniques for imaging traits and genomic data, establishing meaningful connections poses a challenge. We analyzed 86 image features describing tumor characteristics (such as shape and texture) with the underlying transcriptome and post-transcriptome profiles of 22 lung cancer patients (median age 67.5 years, from 42 to 80 years) to unravel the molecular mechanisms behind tumor phenotypes. As a result, we were able to construct a radiogenomic association map (RAM) linking tumor morphology, shape, texture, and size with gene and miRNA signatures, as well as biological correlates of GO terms and pathways. These indicated possible dependencies between gene and miRNA expression and the evaluated image phenotypes. In particular, the gene ontology processes “regulation of signaling” and “cellular response to organic substance” were shown to be reflected in CT image phenotypes, exhibiting a distinct radiomic signature. Moreover, the gene regulatory networks involving the TFs TAL1, EZH2, and TGFBR2 could reflect how the texture of lung tumors is potentially formed. The combined visualization of transcriptomic and image features suggests that radiogenomic approaches could identify potential image biomarkers for underlying genetic variation, allowing a broader view of the heterogeneity of the tumors. Finally, the proposed methodology could also be adapted to other cancer types to expand our knowledge of the mechanistic interpretability of tumor phenotypes.
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Wang, Guoming, Xin Gao, Xueping Wang, Peizhuo Liu, Sophia Lee Guan, Kaijie Qi, Shaoling Zhang, and Chao Gu. "Transcriptome analysis reveals gene associated with fruit size during fruit development in pear." Scientia Horticulturae 305 (November 2022): 111367. http://dx.doi.org/10.1016/j.scienta.2022.111367.

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Wang, Yunfei, Jingjing Chen, Guifeng Wei, Housheng He, Xiaopeng Zhu, Tengfei Xiao, Jiao Yuan, et al. "The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression." Nucleic Acids Research 39, no. 12 (March 4, 2011): 5203–14. http://dx.doi.org/10.1093/nar/gkr102.

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Gong, Wanzhuo, Pengfei Qi, Junbo Du, Xin Sun, Xiaoling Wu, Chun Song, Weiguo Liu, et al. "Transcriptome Analysis of Shade-Induced Inhibition on Leaf Size in Relay Intercropped Soybean." PLoS ONE 9, no. 6 (June 2, 2014): e98465. http://dx.doi.org/10.1371/journal.pone.0098465.

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41

Qiao, Shuting, Yufei Xu, Qizan Hu, Wenqi Dong, Shengmi He, Xingjiang Qi, and Yuyan Sun. "Transcriptome Analysis of Sponge Gourd (Luffa cylindrica) Reveals Candidate Genes Associated with Fruit Size." Agronomy 12, no. 8 (July 30, 2022): 1810. http://dx.doi.org/10.3390/agronomy12081810.

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Sponge gourd belongs to the Cucurbitaceae family and Luffa genus. It is an economically valuable vegetable crop with medicinal properties. The fruit size of sponge gourd presents distinct diversity; however, the molecular insights of fruit size regulation remain uncharacterized. Therefore, two sponge gourd materials with distinct fruit sizes were selected for a comparative transcriptome analysis. A total of 1390 genes were detected as differentially expressed between long sponge gourd (LSG) and short sponge gourd (SSG) samples, with 885 downregulated and 505 upregulated in SSG compared with LSG. KEGG pathway enrichment analysis revealed that the MAPK signaling pathway, biosynthesis of secondary metabolites, and plant hormone signal transduction were significantly enriched. The DEGs involved in the cell cycle and cell division, plant hormone metabolism, and MAPK signal transduction were crucial for sponge gourd fruit size regulation. Additionally, the transcription factor families of ERF, NAC, bHLH, MYB, WRKY, and MADS-box were associated with fruit size regulation. The qRT-PCR validation for selected DEGs were generally consistent with the RNA-Seq results. These results obtained the candidate genes and pathways associated with fruit size and lay the foundation for revealing the molecular mechanisms of fruit size regulation in sponge gourd.
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Roelofs, Dick, Sunday Makama, Tjalf E. de Boer, Riet Vooijs, Cornelis A. M. van Gestel, and Nico W. van den Brink. "Surface coating and particle size are main factors explaining the transcriptome-wide responses of the earthworm Lumbricus rubellus to silver nanoparticles." Environmental Science: Nano 7, no. 4 (2020): 1179–93. http://dx.doi.org/10.1039/c9en01144g.

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Meng, Di, Liyuan Zhang, Jie Meng, Qiaopeng Tian, Lixin Zhai, Zhikui Hao, Zhengbing Guan, Yujie Cai, and Xiangru Liao. "Evaluation of the Strain Bacillus amyloliquefaciens YP6 in Phoxim Degradation via Transcriptomic Data and Product Analysis." Molecules 24, no. 21 (November 5, 2019): 3997. http://dx.doi.org/10.3390/molecules24213997.

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Phoxim, a type of organophosphorus pesticide (OP), is widely used in both agriculture and fisheries. The persistence of phoxim has caused serious environmental pollution problems. In this study, Bacillus amyloliquefaciens YP6 (YP6), which is capable of promoting plant growth and degrading broad-spectrum OPs, was used to study phoxim degradation. Different culture media were applied to evaluate the growth and phoxim degradation of YP6. YP6 can grow rapidly and degrade phoxim efficiently in Luria–Bertani broth (LB broth) medium. Furthermore, it can also utilize phoxim as the sole phosphorus source in a mineral salt medium. Response surface methodology was performed to optimize the degradation conditions of phoxim by YP6 in LB broth medium. The optimum biodegradation conditions were 40 °C, pH 7.20, and an inoculum size of 4.17% (v/v). The phoxim metabolites, O,O-diethylthiophosphoric ester, phoxom, and α-cyanobenzylideneaminooxy phosphonic acid, were confirmed by liquid chromatography–mass spectrometry. Meanwhile, transcriptome analysis and qRT-PCR were performed to give insight into the phoxim-stress response at the transcriptome level. The hydrolase-, oxidase-, and NADPH-cytochrome P450 reductase-encoding genes were significantly upregulated for phoxim hydrolysis, sulfoxidation, and o-dealkylation. Furthermore, the phoxim biodegradation pathways by YP6 were proposed, for the first time, based on transcriptomic data and product analysis.
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Lu, Yuan, Charlotte M. Klimovich, Kalen Z. Robeson, William Boswell, Oscar Ríos-Cardenas, Ronald B. Walter, and Molly R. Morris. "Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fishXiphophorus multilineatus." PeerJ 5 (May 2, 2017): e3275. http://dx.doi.org/10.7717/peerj.3275.

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BackgroundNutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional programming. The live-bearing fishXiphophorus multilineatushas the potential to be a new model for understanding these mechanisms, given prior evidence of nutritional programming influencing behavior and juvenile growth rate. We tested the hypotheses that nutritional programming would influence behaviors involved in energy homeostasis as well gene expression inX. multilineatus.MethodsWe first examined the influence of both juvenile environment (varied in nutrition and density) and adult environment (varied in nutrition) on behaviors involved in energy acquisition and energy expenditure in adult maleX. multilineatus. We also compared the behavioral responses across the genetically influenced size classes of males. Males stop growing at sexual maturity, and the size classes of can be identified based on phenotypes (adult size and pigment patterns). To study the molecular signatures of nutritional programming, we assembled ade novotranscriptome forX. multilineatususing RNA from brain, liver, skin, testis and gonad tissues, and used RNA-Seq to profile gene expression in the brains of males reared in low quality (reduced food, increased density) and high quality (increased food, decreased density) juvenile environments.ResultsWe found that both the juvenile and adult environments influenced the energy intake behavior, while only the adult environment influenced energy expenditure. In addition, there were significant interactions between the genetically influenced size classes and the environments that influenced energy intake and energy expenditure, with males from one of the four size classes (Y-II) responding in the opposite direction as compared to the other males examined. When we compared the brains of males of the Y-II size class reared in a low quality juvenile environment to males from the same size class reared in high quality juvenile environment, 131 genes were differentially expressed, including metabolism and appetite master regulatoragrpgene.DiscussionOur study provides evidence for nutritional programming inX. multilineatus, with variation across size classes of males in how juvenile environment and adult diet influences behaviors involved in energy homeostasis. In addition, we provide the first transcriptome ofX. multilineatus, and identify a group of candidate genes involved in nutritional programming.
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Lawrence, Amanda, Shadaesha Green, Tao Wang, Tsvetan Bachvaroff, and J. Sook Chung. "Seasonal changes in the expression of insulin-like androgenic hormone (IAG) in the androgenic gland of the Jonah crab, Cancer borealis." PLOS ONE 17, no. 2 (February 3, 2022): e0261206. http://dx.doi.org/10.1371/journal.pone.0261206.

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Harvesting the adult male Jonah crab, Cancer borealis, mainly based on the size, has become an economically significant fishery, particularly in the Southern New England region of the US since 2000. Many decapod crustacean fisheries including C. borealis rely on harvesting adult males. Understanding the size related-sexual maturity and the seasonal changes in male reproductive activity is critical for sustainable management. In other decapods, an insulin-like hormone produced by the male-specific androgenic gland (AG), called insulin-like androgenic gland factor (IAG), plays an essential role in sexual maturity. Specifically IAG is involved in developing male primary and secondary sexual characteristics including spermatogenesis. This study aimed first to identify the IAG, then examine if season influences IAG expression in C. borealis males. Finally, the AG transcriptome was used to test if eyestalk neuropeptides regulate IAG levels via an endocrine axis between the two endocrine tissues as established in other crustaceans. The full-length CabIAG sequence is 928 nucleotides long, encoding a 151 amino acid deduced sequence. The CabIAG identified from the AG transcriptome after eyestalk ablation was the most highly expressed gene and accounted for up to 25% of transcripts, further confirming the presence of an endocrine axis between the androgenic gland and eyestalk ganglia. This gene expression was exclusive in male C. borealis AG. The transcriptomic analysis also revealed strong upregulation of the PPOAE transcript and downregulation of proteolytic enzymes. The CabIAG levels differ by season, increasing AG activity in fall and possibly coinciding with high mating activity. The timing of increased AG activity correlating to mating with females should be considered for better stock management for the C. borealis population.
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Queen, Rachel, Moira Crosier, Lorraine Eley, Janet Kerwin, Jasmin E. Turner, Jianshi Yu, Ahlam Alqahtani, et al. "Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves." PLOS Genetics 19, no. 11 (November 27, 2023): e1010777. http://dx.doi.org/10.1371/journal.pgen.1010777.

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Abnormalities of the arterial valves, including bicuspid aortic valve (BAV) are amongst the most common congenital defects and are a significant cause of morbidity as well as predisposition to disease in later life. Despite this, and compounded by their small size and relative inaccessibility, there is still much to understand about how the arterial valves form and remodel during embryogenesis, both at the morphological and genetic level. Here we set out to address this in human embryos, using Spatial Transcriptomics (ST). We show that ST can be used to investigate the transcriptome of the developing arterial valves, circumventing the problems of accurately dissecting out these tiny structures from the developing embryo. We show that the transcriptome of CS16 and CS19 arterial valves overlap considerably, despite being several days apart in terms of human gestation, and that expression data confirm that the great majority of the most differentially expressed genes are valve-specific. Moreover, we show that the transcriptome of the human arterial valves overlaps with that of mouse atrioventricular valves from a range of gestations, validating our dataset but also highlighting novel genes, including four that are not found in the mouse genome and have not previously been linked to valve development. Importantly, our data suggests that valve transcriptomes are under-represented when using commonly used databases to filter for genes important in cardiac development; this means that causative variants in valve-related genes may be excluded during filtering for genomic data analyses for, for example, BAV. Finally, we highlight “novel” pathways that likely play important roles in arterial valve development, showing that mouse knockouts of RBP1 have arterial valve defects. Thus, this study has confirmed the utility of ST for studies of the developing heart valves and broadens our knowledge of the genes and signalling pathways important in human valve development.
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Zhang, Pu, Zhiya Yang, Shihao Jia, Guoliang Chen, Nannan Li, Benjamin Karikari, and Yongce Cao. "Genome-Wide Association Study and Candidate Gene Mining of Seed Size Traits in Soybean." Agronomy 14, no. 6 (May 30, 2024): 1183. http://dx.doi.org/10.3390/agronomy14061183.

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Abstract:
Seed size traits, including seed length (SL), seed width (SW), and seed thickness (ST), are crucial appearance parameters that determine soybean seed weight, yield, and ultimate utilization. However, there is still a large gap in the understanding of the genetic mechanism of these traits. Here, 281 soybeans were utilized to analyze the genetic architecture of seed size traits in different years through multiple (single-locus and multi-locus) genome-wide association study (GWAS) models, and candidate genes were predicted by integrating information on gene function and transcriptome sequencing data. As a result, two, seven, and three stable quantitative trait nucleotides (QTNs) controlling SL, SW, and ST were detected in multiple environments using the single-locus GWAS model, and concurrently detected by the results of the multi-locus GWAS models. These stable QTNs are located on 10 linkage disequilibrium blocks, with single genome regions ranging in size from 20 to 440 kb, and can serve as the major loci controlling soybean seed size. Furthermore, by combining gene functional annotation and transcriptome sequencing data of seeds at different developmental stages from two extreme soybean accessions, nine candidate genes, including Glyma.05G038000, Glyma.05G244100, Glyma.05G246900, Glyma.07G070200, Glyma.11G010000, Glyma.11G012400, Glyma.17G165500, Glyma.17G166500, and Glyma.20G012600 within the major loci that may regulate soybean seed size, were mined. Overall, these findings offer valuable insights for molecular improvement breeding as well as gene functional studies to unravel the mechanism of soybean seed size.
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Gonella-Diaza, Angela María, Sónia Cristina da Silva Andrade, Mariana Sponchiado, Guilherme Pugliesi, Fernando Silveira Mesquita, Veerle Van Hoeck, Ricardo de Francisco Strefezzi, Gustavo R. Gasparin, Luiz L. Coutinho, and Mario Binelli. "Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle." PLOS ONE 10, no. 12 (December 23, 2015): e0145321. http://dx.doi.org/10.1371/journal.pone.0145321.

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Zhang, Yiyao, Aining Zhang, Wenhui Yang, Xinyi Jia, Qingjun Fu, Tingting Zhao, Jingbin Jiang, Jingfu Li, Huanhuan Yang, and Xiangyang Xu. "Transcriptome Analysis and Screening of Genes Associated with Flower Size in Tomato (Solanum lycopersicum)." International Journal of Molecular Sciences 23, no. 24 (December 9, 2022): 15624. http://dx.doi.org/10.3390/ijms232415624.

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Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production. Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and gene expression level of tomato flower development. In this study, RNA-seq analysis was performed on two stages of tomato flower development using the Illumina sequencing platform. A total of 8536 DEGs were obtained by sequencing, including 3873 upregulated DEGs and 4663 down-regulated DEGs. These differentially expressed genes are related to plant hormone signaling, starch and sucrose metabolism. The pathways such as pentose, glucuronate interconversion, and Phenylpropanoid biosynthesis are closely related and mainly involved in plant cellular and metabolic processes. According to the enrichment analysis results of DEGs, active energy metabolism can be inferred during flower development, indicating that flower development requires a large amount of energy and material supply. In addition, some plant hormones, such as GA, may also have effects on flower development. Combined with previous studies, the expression levels of Solyc02g087860 and three of bZIPs were significantly increased in the full flowering stage compared with the flower bud stage, indicating that these genes may be closely related to flower development. These genes were previously reported in Arabidopsis but not in tomatoes. Our next work will conduct a detailed functional analysis of the identified bZIP family genes to characterize their association with tomato flower size. This study will provide new genetic resources for flower formation and provide a basis for tomato yield breeding.
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Zheng, Yuxin, Qilong Ma, Lianzhen Mao, Zhuoxuan Wu, Zhoubin Liu, Xuexiao Zou, and Bozhi Yang. "Comparative Transcriptome Analysis Identified Genes Associated with Fruit Size in Pepper (Capsicum annuum L.)." Horticulturae 9, no. 9 (September 7, 2023): 1009. http://dx.doi.org/10.3390/horticulturae9091009.

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Pepper (Capsicum annuum L.) is one of the most widely grown vegetable crops in China, with widespread cultivation worldwide. Fruit weight (size) is a complex trait controlled by multiple factors and is an essential determinant of pepper yield. In this study, we analyzed the transcriptome of two pepper recombinant lines with different fruit weights, ‘B302’ and ‘B400’, at five developmental stages to reveal some of the differentially expressed genes and mechanisms controlling fruit weight. The results showed that 21,878 differential genes were identified between the two specimens. Further analysis of the differentially expressed genes revealed that Boron transporter 4 was significantly highly expressed in the large-fruited pepper and almost not expressed at all in the small-fruited pepper. CaAUX1, CaAUX/IAA, CaGH3, CaSAUR, and other related genes in the Auxin signal transduction pathway were highly expressed in the large-fruited pepper but significantly reduced in the small-fruited pepper. In addition, a comparison of differentially expressed transcription factors at different times revealed that transcription factors such as CaMADS3, CaAGL8, CaATHB13, and CaATHB-40 were highly differentially expressed in the large-fruited pepper, and these transcription factors may be related to pepper fruit expansion. Through weighted gene co-expression network analysis (WGCNA), the MEorangered4 module was shown to have a highly significant correlation with fruit weight, and the key modules were analyzed by constructing the hub core gene network interactions map and core genes regulating fruit weight such as APETALA 2 were found. In conclusion, we find that the expression of relevant genes at different developmental stages was different in ‘B302’ and ‘B400’, and it was hypothesized that these genes play essential roles in the development of fruit size and that the interactions occurring between transcription factors and phytohormones may regulate the development of fruit size.

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