Relevant bibliographies by topics / Whole-transcriptome sequencing

Academic literature on the topic 'Whole-transcriptome sequencing'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Whole-transcriptome sequencing"

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Streets, A. M., X. Zhang, C. Cao, Y. Pang, X. Wu, L. Xiong, L. Yang, et al. "Microfluidic single-cell whole-transcriptome sequencing." Proceedings of the National Academy of Sciences 111, no. 19 (April 29, 2014): 7048–53. http://dx.doi.org/10.1073/pnas.1402030111.

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Hosokawa, Kohei, Sachiko Kajigaya, Keyvan Keyvanfar, Wangmin Qiao, Yanling Xie, Angelique Biancotto, Danielle M. Townsley, Xingmin Feng, and Neal S. Young. "Whole transcriptome sequencing identifies increasedCXCR2expression in PNH granulocytes." British Journal of Haematology 177, no. 1 (February 1, 2017): 136–41. http://dx.doi.org/10.1111/bjh.14502.

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Yang, In Seok, and Sangwoo Kim. "Analysis of Whole Transcriptome Sequencing Data: Workflow and Software." Genomics & Informatics 13, no. 4 (2015): 119. http://dx.doi.org/10.5808/gi.2015.13.4.119.

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Petrini, Iacopo, Arun Rajan, Trung Pham, Donna Voeller, Sean Davis, James Gao, Yisong Wang, and Giuseppe Giaccone. "Whole Genome and Transcriptome Sequencing of a B3 Thymoma." PLoS ONE 8, no. 4 (April 5, 2013): e60572. http://dx.doi.org/10.1371/journal.pone.0060572.

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Siezen, Roland J., Greer Wilson, and Tilman Todt. "Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays." Microbial Biotechnology 3, no. 2 (February 22, 2010): 125–30. http://dx.doi.org/10.1111/j.1751-7915.2010.00166.x.

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Ruan, Miaomiao, Jiying Liu, Xueyang Ren, Chu Li, Allan Z. Zhao, Lin Li, Haiyuan Yang, Yifan Dai, and Ying Wang. "Whole transcriptome sequencing analyses of DHA treated glioblastoma cells." Journal of the Neurological Sciences 396 (January 2019): 247–53. http://dx.doi.org/10.1016/j.jns.2018.11.027.

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Seliger, Sonja, Verena Geirhos, Torsten Haferlach, Wolfgang Kern, Wencke Walter, Manja Meggendorfer, Constance Baer, Anna Stengel, and Claudia Haferlach. "Comprehensive Analysis of MYC Translocations in Multiple Myeloma By Whole Genome Sequencing and Whole Transcriptome Sequencing." Blood 134, Supplement_1 (November 13, 2019): 1774. http://dx.doi.org/10.1182/blood-2019-124704.

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Background 8q24 translocations leading to overexpression of MYC are an established prognostic marker in multiple myeloma (MM). Currently FISH (fluorescence in situ hybridization) on CD138+ enriched cell population is the standard diagnostic approach to evaluate the presence of 8q24 translocations. Due to the heterogeneity of breakpoints and technical issues the design of FISH probes is challenging and so far no single FISH assay is capable of detecting each translocation. Aims (1) Evaluation of the frequency of 8q24 translocations in MM by whole genome sequencing (WGS). (2) Determination of the breakpoints on 8q24 and partners. (3) Correlation of WGS data with FISH and MYC expression determined by whole transcriptome sequencing (WTS). Patient cohort and methods CD138+ cell fractions were selected by MACS from bone marrow aspirate samples of 264 patients diagnosed with MM. FISH, WGS and WTS were performed in all cases. For WGS, 151bp paired-end sequences where generated on NovaSeq 6000 machines (Illumina, San Diego, CA). All reported p-values are two-sided and were considered significant at p<0.05. For gene expression (GE) analysis by WTS, estimated gene counts were normalized and the resulting log2 counts per million were used as a proxy of gene expression in each sample. For artefact exclusion, structural variants were checked against 4386 cases covering the spectrum of hematological malignancies. Results In 91/264 (34%) of cases, at least one rearrangement involving the MYC locus (MYCr) was detected by WGS. In 18 of these samples (20%), >1 MYCr was present (114 MYCr in total). Out of these 91 patients, in 32 (35%) the MYCr had been identified by FISH, in 46 cases (51%) it was not detected due to the heterogeneity of breakpoints, while in 13 (14%) patients FISH could not be evaluated (e.g. due to insufficient patient material). Of the 114 MYCr encountered in WGS, 42 involved one of the immunoglobulin loci (IGH n=25, IGK n=9, IGL n=8). The remaining 72 MYCr involved other rare partners. In 29 of these rearrangements, as well as in four complex rearrangements involving IGH or IGK, recurrent rare partners were identified, comprising 1p12/FAM46C (n=6), 6p24.3/BMP6 (n=10), 6q21/FOXO3 (n=4), 7p21.3 (n=3), 11q13/CCND1 (n=5), 20q11.22 (n=5). 43 MYCr involved non-recurrent (single) rare partners, for 4 of these a MYCr was also detected by FISH. The MYCr detected were rather complex: only 34 (30%) showed a simple reciprocal translocation (IGH n=7, IGL n=2, IGK n=4, rare partners n=21), 60 (53%) showed more complex rearrangements (IGH n=12, IGL n=4, IGK n=2, rare partners n=42) and in 20 cases (18%) at least one additional chromosome was involved (IGH n=6, IGL n=3, IGK n=2, rare partners n=9). In 80% of MYCr, breakpoints were located between genomic positions 128.203.605 and 129.375.490 encompassing the pre-described MYC surrounding locus PVT1. IGH-MYC rearrangements showed a tendency to cluster towards the centromere. MYCr involving rare partners showed the broadest breakpoint spectrum and clustered in both directions of the hotspot (Fig 1A). Regarding expression of MYC, all cases showed an overexpression (median GE: 6.9 vs 4.5 in normal controls). Median GE was similar in cases with Ig partners (IGH: 7.1, IGL: 6.7, IGK: 6.6) and non Ig partners (6.8) and also in cases with MYCr detected by FISH (7.0) and cases in which it was not detected by FISH (6.5). Analysis of additional chromosomal aberrations revealed that hyperdiploidy was significantly more frequent in MYCr (n=68/91, 75% vs n=76/173, 44%; p=0.001), while t(11;14) was found significantly less frequent (n=11/91, 12% vs n=49/173, 28%; p=0.003) (Fig 1B). No associations were found between MYCr and other frequent chromosomal abnormalities. Furthermore, molecular mutations frequently occurring in MM (ATM, BRAF, KRAS, NRAS, TP53, IRF4) were analyzed, revealing that patients with MYCr were significantly less frequently associated with mutations in the IRF4 gene (MYCr patients n=1/91; non-MYCr patients n=13/173; p =0.028) (Fig 1C). Conclusions (1) WGS detects ~3x more MYCr compared to FISH. (2) The complexity on the genomic level of MYCr is high, therefore the detection with targeted assays is limited while WGS allows a more comprehensive analysis. (3) MYC expression in cases with MYCr with non Ig partners is comparably high as for Ig-MYC translocations. (4) MYCr are associated with hyperdiploidy, whereas t(11;14) and IRF4 mutations were detected at a lower frequency. Disclosures Seliger: MLL Munich Leukemia Laboratory: Employment. Geirhos:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Walter:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Baer:MLL Munich Leukemia Laboratory: Employment. Stengel:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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Cirulli, Elizabeth T., Abanish Singh, Kevin V. Shianna, Dongliang Ge, Jason P. Smith, Jessica M. Maia, Erin L. Heinzen, James J. Goedert, and David B. Goldstein. "Screening the human exome: a comparison of whole genome and whole transcriptome sequencing." Genome Biology 11, no. 5 (2010): R57. http://dx.doi.org/10.1186/gb-2010-11-5-r57.

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Martin, Jeffrey, Wenhan Zhu, Karla D. Passalacqua, Nicholas Bergman, and Mark Borodovsky. "Bacillus anthracis genome organization in light of whole transcriptome sequencing." BMC Bioinformatics 11, Suppl 3 (2010): S10. http://dx.doi.org/10.1186/1471-2105-11-s3-s10.

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Tang, Wei, and Ludmila Prokunina-Olsson. "Whole transcriptome sequencing of normal and tumor bladder tissue samples." Genome Biology 12, Suppl 1 (2011): P23. http://dx.doi.org/10.1186/gb-2011-12-s1-p23.

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Dissertations / Theses on the topic "Whole-transcriptome sequencing"

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Khan, Hamza. "De novo annotation of non-model organisms using whole genome and transcriptome shotgun sequencing." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/60152.

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Clouse, Jared William. "The Amaranth (Amaranthus Hypochondriacus) Genome: Genome, Transcriptome and Physical Map Assembly." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5916.

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Amaranthus hypochondriacus is an emerging pseudo-cereal native to the New World which has garnered increased attention in recent years due to its nutritional quality, in particular its seed protein, and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleotetraploid that shows amphidiploid inheritance (2n=32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth A. hypochondriacus. The genome assembly consisted of 377 Mb in 3,518 scaffolds with an N50 of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which Copia-like elements were the most common classified retrotransposon. A transcriptome, consisting of 66,370 contigs, was assembled from eight different tissue and abiotic stress libraries. Annotation of the genome identified 23,059 genes that were supported by our de novo transcriptome assembly, the RefBeet 1.1 gene index and the Uniprot_sprot database. To describe the genetic diversity within the grain amaranths (A. hypochondriacus, A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) we re-sequenced seven accessions in the genus Amaranthus (four A. hypochondriacus, and one of each A. caudatus, A. cruentus, and A. hybridus), which identified 7,184,636 and 1,760,433 interspecific and intraspecific single nucleotide polymorphisms, respectively. A phylogeny analysis of the re-sequenced accessions substantiated the classification of A. hybridus as the progenitor species of the grain amaranths. Lastly, we generated a physical map for A. hypochondriacus using the BioNano optical mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano optical genome maps nearly doubled the N50 of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and Beta vulgaris (sugar beet) and estimated, using Ks analysis, the age of the most recent polyploidization event in amaranth.
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Raykova, Doroteya. "Genetics of Two Mendelian Traits and Validation of Induced Pluripotent Stem Cell (iPSC) Technology for Disease Modeling." Doctoral thesis, Uppsala universitet, Medicinsk genetik och genomik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-246228.

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Novel technologies for genome analysis have provided almost unlimited opportunities to uncover structural gene variants behind human disorders. Whole exome sequencing (WES) is especially useful for understanding rare Mendelian conditions, because it reduces the requirements for a priori clinical data, and can be applied on a small number of patients. However, supporting functional data on the effect of specific gene variants are often required to power these findings. A variety of methods and biological model systems exists for this purpose. Among those, induced pluripotent stem cells (iPSCs), which are capable of self-renewal and differentiation, stand out as an alternative to animal models. In papers I and II we took advantage of WES to identify gene variants underlying autosomal recessive pure hair and nail ectodermal dysplasia (AR PHNED) as well as autosomal dominant familial visceral myopathy (FVM). We identified a homozygous variant c.821T>C (p.Phe274Ser) in the KRT74 gene as the causative mutation in AR PHNED, supported by the fact that Keratin-74 was undetectable in hair follicles of an affected family member. In a family segregating FVM we found a heterozygous tandem base substitution c.806_807delinsAA (p.(Gly269Glu)) in the ACTG2 gene in the affected members. This novel variant is associated with a broad range of visceral symptoms and a variable age of onset. In Paper III we explored the similarity between clonally derived iPSC lines originating from a single parental fibroblast line and we highlighted the necessity to use lines originating from various donors in disease modeling because of biological variation. Paper IV focused on how the genomic integrity of iPSCs is affected by the choice of reprogramming methods. We described several novel cytogenetic rearrangements in iPSCs and we identified a chromosome 5q duplication as a candidate aberration for growth advantage. In summary, this doctoral thesis brings novel findings on unreported disease-causing variants, as supported by extensive genetic analysis and functional data. A novel molecular mechanism behind AR PHNED is presented and the phenotypic spectrum associated with FVM is expanded. In addition, the thesis brings novel understanding of benefits and limitations of the iPSC technology to be considered for disease modeling.
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BARZAGO, CLAUDIA. "Identification of a new molecular signature in peripheral blood mononuclear cells from patients affected by myasthenia gravis." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2016. http://hdl.handle.net/10281/105298.

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La miastenia grave è una malattia autoimmune T-dipendente mediata da autoanticorpi diretti contro proteine della giunzione neuromuscolare. È caratterizzata da un danno alla trasmissione neuromuscolare che causa affaticamento e debolezza muscolare. In circa l’80% dei pazienti, la malattia è associata alla produzione di autoanticorpi diretti contro il recettore dell’acetilcolina (AChR) localizzato a livello della membrana post-sinaptica della giunzione neuromuscolare. Numerose evidenze sperimentali suggeriscono che il processo autoimmune si sviluppi nel timo; tuttavia, i meccanismi molecolari sottostanti la perpetuazione di tali processi in periferia non sono del tutto noti. Abbiamo studiato, mediante sequenziamento dell’intero trascrittoma, il profilo trascrizionale delle cellule mononucleate da sangue periferico derivate da pazienti miastenici ad esordio precoce di malattia (minore di 50 anni di età) e positivi per gli anticorpi anti-AChR (AChR-EOMG), che rappresentano il sottogruppo clinico meglio studiato. Come controllo, sono state incluse nello studio cellule derivate da individui sani di pari età e sesso. I risultati di trascrittomica combinati con l’analisi dei pathway, tramite il software Ingenuity, hanno mostrato che 128 trascritti codificanti e 9 precursori di microRNAs (miRNAs) erano differenzialmente espressi tra pazienti AChR-EOMG e controlli. In particolare, 22 su 128 (17%) trascritti codificanti appartenevano alla categoria ‘malattie infettive’ e 59 su 128 (46%) alle categorie ‘malattie infiammatorie’ e ‘risposta infiammatoria’. La validazione dei livelli di espressione dei trascritti tramite qPCR ha mostrato che, tra i trascritti associati a ‘malattie infettive’, i livelli di espressione di ETF1, NFKB2, PLK3 e PPP1R15A erano aumentati, mentre quelli di CLC ed IL4 erano diminuiti nei pazienti AChR-EOMG rispetto ai controlli; nella categoria ‘infiammazione’, i livelli di espressione di ABCA1, FUS e RELB erano aumentati, suggerendo una perdita delle funzioni immunomodulatorie di queste molecole. Partendo dai dati di trascrittomica abbiamo inoltre applicato una selezione sulla base delle interazioni putative tra miRNAs e trascritti target. La successiva validazione tramite qPCR ha mostrato che i livelli di espressione dei miRNA miR-612, miR-3654 e miR-3651 erano aumentati, mentre i target predetti di miR-612, AKAp12 e HRH4, come anche il target putativo di miR-3651, CRISP3, erano diminuiti nei pazienti AChR-EOMG, ad ulteriore sostegno dell'ipotesi di un’alterazione dei processi di immunoregolazione in periferia. In conclusione, abbiamo identificato un nuovo profilo molecolare associato ad AChR-EOMG, dimostrando un ruolo cruciale di molecole associate ad ‘infezione’ ed ‘infiammazione’ nella patogenesi della miastenia grave. Ulteriori indagini sulle molecole scoperte in questo studio potranno contribuire ad una migliore conoscenza delle basi molecolari della patogenesi della malattia con un possibile impatto su nuove strategie terapeutiche.
Myasthenia gravis (MG) is a T-cell dependent humoral-mediated autoimmune disease characterized by neuromuscular transmission impairment, resulting in fatigability and muscular weakness. In approximately 80% of MG patients, the disorder is associated with the production of autoantibodies against acetylcholine receptor (AChR) localized at the post-synaptic membrane of the neuromuscular junction. Growing body of evidences suggests that the autoimmune reaction develops in the thymus; nevertheless, the molecular mechanisms underlying the perpetuation of the autoimmune processes in the periphery are not fully characterized. We studied the transcriptional profile of peripheral blood mononuclear cells from AChR-positive early onset (< 50 years old) (AChR-EOMG) patients, the best studied clinical subgroup, and age- and sex-matched healthy controls, by using whole-transcriptome sequencing. Transcriptome data together with Ingenuity Pathway Analysis showed that 128 coding transcripts and 9 microRNA (miRNAs) precursors were differentially expressed between AChR-EOMG patients and healthy controls. In particular, 17% (22 out of 128) of the coding transcripts were related to ‘infectious disease’ category and 46% (59 out of 128) to ‘inflammatory disease’ and ‘inflammatory response’ categories. Selection of the genes of interest and further qPCR validation of the transcript levels revealed that among the ‘infectious disease-associated’ transcripts, ETF1, NFKB2, PLK3, and PPP1R15A were increased, whereas CLC and IL4 were decreased in AChR-EOMG patients versus healthy controls; in the ‘inflammation’ categories, ABCA1, FUS, and RELB were upregulated, suggesting of a possible loss of immunomodulatory function. Additional transcriptome data analysis and validation were also centered on miRNA-mRNA putative interactions. We observed that miR-612, miR-3651, and miR-3654 were upregulated, whereas miR-612-putative AKAp12 and HRH4 target transcripts and also miR-3651-predicted CRISP3 target were decreased in AChR-EOMG samples, further suggesting a loss of immunoregulatory processes. Taken together, our findings disclose a novel peripheral molecular signature associated with AChR-EOMG, and suggest a key role of ‘infectious’ and ‘inflammation-related’ molecules in disease pathogenesis. Future studies on the molecules discovered here will allow a better understanding of the molecular basis of AChR-EOMG pathogenesis that could be helpful for the development of new therapeutic interventions.
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Burkert, Christian Martin. "Cis-regulation and genetic control of gene expression in neuroblastoma." Doctoral thesis, Humboldt-Universität zu Berlin, 2021. http://dx.doi.org/10.18452/23008.

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Genregulation beeinflusst Phänotypen im Kontext von Gesundheit und Krankheit. In Krebszellen regulieren genetische und epigenetische Faktoren die Genexpression in cis. Das Neuroblastom ist eine Krebserkrankung, die häufig im Kindesalter auftritt. Es ist gekennzeichnet durch eine geringe Anzahl exonischer Mutationen und durch häufige Veränderungen der somatischen Kopienzahl, einschließlich Genamplifikationen auf extrachromosomaler zirkulärer DNA. Bisher ist wenig darüber bekannt, wie lokale genetische und epigenetische Faktoren Gene im Neuroblastom regulieren. In dieser Arbeit kombiniere ich die allelspezifische Analyse ganzer Genome (WGS), Transkriptome und zirkulärer DNA von Neuroblastom-Patienten, um genetische und cis-regulatorische Effekte zu charakterisieren. Ich zeige, dass somatische Dosis-Effekte der Kopienzahl andere lokale genetische Effekte dominieren und wichtige Signalwege regulieren. Genamplifikationen zeigen starke Dosis-Effekte und befinden sich häufig auf großen extrachromosomalen zirkulären DNAs. Die vorgestellte Analyse zeigt, dass der Verlust von 11q zu einer Hochregulation von Histonvarianten H3.3 und H2A in Tumoren mit alternativer Verlängerung der Telomere (ALT) führt, und dass erhöhte somatische Kopienzahl die Expression der TERT Gens verstärken können. Weitere Erkenntnisse sind, dass 17p-Ungleichgewichte und die damit verbundene Herunterregulierung neuronaler Gene sowie die Hochregulierung des genomisch geprägten Gens RTL1 durch Kopienzahl-unabhängige allelische Dosis-Effekte mit einer ungünstigen Prognose verbunden sind. Die cis-QTL-Analyse bestätigt eine zuvor beschriebene Regulation des LMO1 Gens durch einen Enhancer-Polymorphismus und charakterisiert das regulatorische Potenzial weiterer GWAS-Risiko-Loci. Die Arbeit unterstreicht die Bedeutung von Dosis-Effekten im Neuroblastom und liefert eine detaillierte Übersicht regulatorischer Varianten, die in dieser Krankheit aktiv sind.
Gene regulation controls phenotypes in health and disease. In cancer, the interplay between germline variation, genetic aberrations and epigenetic factors modulate gene expression in cis. The childhood cancer neuroblastoma originates from progenitor cells of the sympathetic nervous system. It is characterized by a sparsity of recurrent exonic mutations but frequent somatic copy-number alterations, including gene amplifications on extrachromosomal circular DNA. So far, little is known on how local genetic and epigenetic factors regulate genes in neuroblastoma to establish disease phenotypes. I here combine allele-specific analysis of whole genomes, transcriptomes and circular DNA from neuroblastoma patients to characterize genetic and cis-regulatory effects, and prioritize germline regulatory variants by cis-QTLs mapping and chromatin profiles. The results show that somatic copy-number dosage dominates local genetic effects and regulates pathways involved in telomere maintenance, genomic stability and neuronal processes. Gene amplifications show strong dosage effects and are frequently located on large but not small extrachromosomal circular DNAs. My analysis implicates 11q loss in the upregulation of histone variants H3.3 and H2A in tumors with alternative lengthening of telomeres and cooperative effects of somatic rearrangements and somatic copy-number gains in the upregulation of TERT. Both 17p copy-number imbalances and associated downregulation of neuronal genes as well as upregulation of the imprinted gene RTL1 by copy-number-independent allelic dosage effects is associated with an unfavorable prognosis. cis-QTL analysis confirms the previously reported regulation of the LMO1 gene by a super-enhancer risk polymorphism and characterizes the regulatory potential of additional GWAS risk loci. My work highlights the importance of dosage effects in neuroblastoma and provides a detailed map of regulatory variation active in this disease.
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Tan, Yuxiang. "Computational approaches for whole-transcriptome cancer analysis based on RNA sequencing data." Thesis, 2016. https://hdl.handle.net/2144/14502.

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RNA-Seq (Whole Transcriptome Shotgun Sequencing) provides an ideal platform to study the complete set of transcripts for a specific developmental stage or physiological condition. It reveals not only expression-level changes, but also structural changes in the coding sequences, including gene rearrangements. In this dissertation, I present my contributions to the development of computational tools for the robust and efficient analysis of RNA-seq data to support cancer research. To automate the laborious and computationally intensive procedure of RNA-seq data management, I worked on the development of Hydra, an RNA-seq pipeline for the parallel processing and quality control of large numbers of samples. With user-friendly reports on quality control and running checkpoints, Hydra makes the data processing procedure fast, efficient and reliable. Here, I report my application of the pipeline to the analysis of patient-derived lymphoma xenograft samples, to show Hydra’s ability to detect abnormalities (e.g., mouse tissue contamination) in the sequencing data. Because fusions play an important role in carcinogenesis, fusion detection has become an important area of methodological research. Several computational methods have been developed to identify fusion transcripts from RNA-seq data. However, all these methods require realignment to the transcriptome, a computationally expensive task, unnecessary in many cases. Here, I present QueryFuse, a novel gene-specific fusion-detection algorithm for aligned RNA-seq data. It is designed to help biologists find and/or computationally validate fusions of interest quickly, and to annotate the detected events with visualization and detailed properties of the supporting reads. By focusing the fusion detection on read pairs aligned to query genes, we can not only reduce realignment time, but also afford to use a more accurate but computationally expensive local aligner. In the extensive evaluation I performed, I obtained comparable or better results compared with two widely adopted tools (deFuse and TophatFusion) on two simulated datasets, as well as on cell line datasets with known fusions. Finally, I contributed to the identification of a novel fusion event in lymphoma, with potential therapeutic implications in clinical samples. I validated this fusion in silico by my putative reference method before experimental validation.
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Lin, Kuan-Ting, and 林冠廷. "Identification of latent biomarkers in hepatocellular carcinoma by ultra-deep whole-transcriptome sequencing." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/97773695842537346649.

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博士
國立陽明大學
生物醫學資訊研究所
102
There is an urgent need to identify biomarkers for hepatocellular carcinoma due to limited treatment options and the poor prognosis of this common lethal disease. Whole-transcriptome shotgun sequencing (RNA-Seq) provides new possibilities for biomarker identification. We sequenced ∼250 million pair-end reads from a pair of adjacent normal and tumor liver samples. With the aid of bioinformatics tools, we determined the transcriptome landscape and sought novel biomarkers by further empirical validations in 55 pairs of adjacent normal and tumor liver samples with various viral statuses such as HBV(+), HCV(+) and HBV(-)HCV(-). We identified a novel gene with coding regions, termed DUNQU1, which has a tissue-specific expression pattern in tumor liver samples of HCV(+) and HBV(-)HCV(-) hepatocellular carcinomas. Overexpression of DUNQU1 in Huh7 cell lines enhances the ability to form colonies in soft agar. Also, we identified three novel differentially-expressed protein-coding genes (ALG1L, SERPINA11 and TMEM82) that lack documented expression profiles in liver cancer and showed that the level of SREPINA11 is correlated with pathology stages. Moreover, we showed that the alternative splicing event of FGFR2 is associated with virus infection, tumor size, cirrhosis and tumor recurrence. The findings indicate that these new markers of hepatocellular carcinoma may be of value in improving prognosis and could have potential as new targets for developing new treatment options.
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Radovich, Milan. "DECODING THE TRANSCRIPTIONAL LANDSCAPE OF TRIPLE-NEGATIVE BREAST CANCER USING NEXT GENERATION WHOLE TRANSCRIPTOME SEQUENCING." Thesis, 2012. http://hdl.handle.net/1805/2745.

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Indiana University-Purdue University Indianapolis (IUPUI)
Triple-negative breast cancers (TNBCs) are negative for the expression of estrogen (ER), progesterone (PR), and HER-2 receptors. TNBC accounts for 15% of all breast cancers and results in disproportionally higher mortality compared to ER & HER2-positive tumours. Moreover, there is a paucity of therapies for this subtype of breast cancer resulting primarily from an inadequate understanding of the transcriptional differences that differentiate TNBC from normal breast. To this end, we embarked on a comprehensive examination of the transcriptomes of TNBCs and normal breast tissues using next-generation whole transcriptome sequencing (RNA-Seq). By comparing RNA-seq data from these tissues, we report the presence of differentially expressed coding and non-coding genes, novel transcribed regions, and mutations not previously reported in breast cancer. From these data we have identified two major themes. First, BRCA1 mutations are well known to be associated with development of TNBC. From these data we have identified many genes that work in concert with BRCA1 that are dysregulated suggesting a role of BRCA1 associated genes with sporadic TNBC. In addition, we observe a mutational profile in genes also associated with BRCA1 and DNA repair that lend more evidence to its role. Second, we demonstrate that using microdissected normal epithelium maybe an optimal comparator when searching for novel therapeutic targets for TNBC. Previous studies have used other controls such as reduction mammoplasties, adjacent normal tissue, or other breast cancer subtypes, which may be sub-optimal and have lead to identifying ineffective therapeutic targets. Our data suggests that the comparison of microdissected ductal epithelium to TNBC can identify potential therapeutic targets that may lead to be better clinical efficacy. In summation, with these data, we provide a detailed transcriptional landscape of TNBC and normal breast that we believe will lead to a better understanding of this complex disease.
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Lin, Fang-Yu, and 林芳瑜. "Whole Genome Sequencing, Transcriptome Analysis of Acid Response, and Urease Gene Cluster Characterization of Klebsiella pneumoniae CG43." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/72275031070553698724.

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碩士
國立清華大學
分子醫學研究所
101
Klebsiella pneumoniae is an important opportunistic pathogen that causes various human diseases such as pneumonia, urinary tract infection, meningitis, bacteremia and septicemia. In Taiwan, K. pneumoniae is the predominant pathogen responsible for pyogenic liver abscess in diabetic patients and K1 and K2 serotypes account for the majority of the isolates. K. pneumoniae CG43 was originally isolated from a patient with pyogenic liver abscess in Taiwan. It is a highly virulent K2 serotype strain. In this study, the whole genome sequence of K. pneumoniae CG43 was determined and annotated. The genome is 5,166,857 bp in length. The similarity of the CG43 genome sequence with that of K. pneumoniae NTUH-K2044 and MGH 78578 are 93 % and 94 %, respectively. K. pneumoniae CG43 has 203 open reading frames distinct from K. pneumoniae NTUH-K2044 and K. pneumoniae MGH 78578. Furthermore, because the ability of acid resistance is important for Enterobacteriaceae, we also performed transcriptome analysis of K. pneumoniae CG43 gene expression profile under acidic growth conditions. The data indicate that 4.94 % genes in CG43 genome were induced, while 18.34 % genes were repressed. Most of the up-regulated genes are associated with chaperone-related function and many of the down-regulated genes belong to maltose regulon. Besides, there are two urease gene clusters in K. pneumoniae CG43, different from most of K. pneumoniae that has only one urease gene cluster. Urease catalyzes the hydrolysis of the urea into carbon dioxide and ammonia. Besides providing nitrogen sources, the reaction can neutralize acidic environments, allowing pathogenic bacteria to survive the acidic conditions. Three types of urease mutant strains (ΔureA1, ΔureA2 and ΔureA1 ΔureA2) were constructed in CG43. Growth of ΔureA1 and ΔureA1 ΔureA2 double mutant was reduced in M9 minimal medium using urea as the sole nitrogen source. The two mutant strains lack urease activity as determined by Christensen’s Urea Agar. In addition, the growth of wild type and three urease mutant strains has no difference under acidic environment. The result suggests that urease is not a major factor contributing to acid tolerance of K. pneumoniae CG43 under normal cultural condition. To sum up, the complete CG43 genome sequence will provide critical information for future analysis of the virulence factors in the bacterium.
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10

Chow, Anthony. "Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer." Thesis, 2012. http://hdl.handle.net/1807/33381.

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Shortcomings of current methods of prostate cancer detection draw attention to a need for improved biomarkers. The TMPRSS2:ERG gene fusion leads to the overexpression of ERG, an ETS family transcription factor, and is the most prevalent genetic lesion in prostate cancer, but its clinical utility remains to be defined. Two radical prostatectomy samples were analysed by next-generation whole transcriptome sequencing. The chosen samples differed in fusion gene status, as previously determined by RT-PCR. The involvement of novel and previously reported prostate cancer-related transcripts, Wnt signalling, p53 effector loss and several ETS-regulated pathways was identified in the prostate cancer cases examined. ERG was found to directly transactivate RhoGDIB, a gene associated with fusion-positive prostate cancer. Overexpression of RhoGDIB elicited spindle-shaped morphology, faster cell migration and increased cell proliferation, phenotypic changes suggestive of cancer progression. The present findings confirm the value of comprehensive sequencing for biomarker development and indicate avenues of future study.
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Book chapters on the topic "Whole-transcriptome sequencing"

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Benjak, Andrej, Claudia Sala, and Ruben C. Hartkoorn. "Whole-Transcriptome Sequencing for High-Resolution Transcriptomic Analysis in Mycobacterium tuberculosis." In Methods in Molecular Biology, 17–30. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2450-9_2.

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Sinjab, Ansam, Reem Daouk, Wassim Abou-Kheir, and Humam Kadara. "Whole Transcriptome Sequencing Analysis of Cancer Stem/Progenitor Cells Obtained from Mouse Lung Adenocarcinomas." In Methods in Molecular Biology, 187–98. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1278-1_15.

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Detera-Wadleigh, Sevilla D., Nirmala Akula, and Liping Hou. "Basic Molecular Genetics Concepts and Tools." In Psychiatric Genetics, 34–56. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780190221973.003.0003.

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Progress in genetics in the last decades has been spurred largely by the Human Genome Project. Successful sequencing of the human genome and genomes of organisms across the evolutionary scale has been achieved. Scientific discoveries and innovations steered the refinement and annotation of sequences, cataloging of variation including SNPs and CNVs, development of fast, precise, high throughput methods and improved bioinformatics and statistical tools. These advances boosted GWAS on large samples identifying multiple susceptibility loci in diverse complex diseases and traits. Exome, whole genome and RNA sequencing has uncovered intricate elements of coding, noncoding and regulatory regions and the richness of the transcriptome. Evolution in genome editing has heightened the ability to alter any nucleotide and discern its biological effect. Exploiting these innovations in studies involving cells derived from patients through the iPSC technology offers manifold possibilities for functional studies that could enhance disease modeling and yield new therapeutic targets.
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Ali, Irfan, Faiz Ahmad Joyia, Ghulam Mustafa, Safdar Ali Mirza, and Muhammad Sarwar Khan. "Emerging Trends to Improve Tropical Plants: Biotechnological Interventions." In Tropical Plant Species [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.108532.

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Tropical plants are an integral part of the ecosystem and are of significance for the well-being of humanity. Since their domestication in 10,000 BC, conventional breeding has played a crucial role in their conservation and widespread adaptation worldwide. Advancements in multi-omics approaches, that is, genomics, metabolomics, transcriptomics, proteomics, whole genome sequencing, and annotation, have led to the identification of novel genes involved in crucial metabolic pathways, thus helping to develop tropical plant varieties with desirable traits. Information retrieved from the pan-genome, super-pan-genome, and pan-transcriptome has further uplifted marker-assisted selection and molecular breeding. Tissue culture techniques have not only helped to conserve endangered plant species but have also opened up new avenues in terms of mass-scale propagation of ornamental plants. Transgenic technology is increasingly contributing to the betterment of tropical plants, and different plant species have been engineered for valuable traits. Likewise, genome editing is appearing to be a promising tool to develop tropical plants having the potential to fulfill future needs. Hence, this chapter highlights the importance of conventional and modern scientific approaches for the conservation and improvement of tropical plant species.
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Conference papers on the topic "Whole-transcriptome sequencing"

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Darabi, Sourat, Andrew Elliott, David R. Braxton, Jia Zeng, Kelsey Poorman, Jeffrey Swensen, Geoffrey T. Gibney, et al. "Abstract 2221: Whole transcriptome sequencing reveals oncogenic fusions in melanoma." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2221.

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Radovich, Milan, Bradley A. Hancock, Nawal Kassem, Jin Zhu, Jarret Glasscock, Sunil Badve, Yunlong Liu, Kenneth A. Kesler, Patrick J. Loehrer, and Bryan P. Schneider. "Abstract 4858: Next-generation whole transcriptome sequencing of thymic malignancies." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4858.

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Mak, Cathy Ka-Yan, Grace Tin-Yan Chung, Kevin Yuk-Lap Yip, Ken Kai-Yuen Tso, Sau-Dan Lee, Siu-Tim Cheung, Sai-Wah Tsao, Pierre Busson, Ka-Fai To, and Kwok-Wai Lo. "Abstract 3425: Whole-transcriptome analyses of EBV-associated nasopharyngeal carcinoma using next-generation transcriptome sequencing." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-3425.

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Tang, Wei, and Ludmila Prokunina-Olsson. "Abstract 2128: Whole transcriptome sequencing in normal and cancer prostate tissue." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2128.

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Kwon, Nak-Jung, Woo Chung Lee, Jiwoong Kim, Hyeri Kim, Ahreum Seong, Bong Cho Kim, Doo Hyun Park, and Kap-Seok Yang. "Abstract 3574: Analysis of whole genome and transcriptome sequencing in single cell." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-3574.

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Kohno, Takashi, Hitoshi Ichikawa, Yasushi Totoki, Kazuki Yasuda, Masaki Hiramoto, Takao Nammo, Hiromi Sakamoto, et al. "Abstract B93: Gene fusions detected by whole transcriptome sequencing of lung adenocarcinoma." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Nov 12-16, 2011; San Francisco, CA. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1535-7163.targ-11-b93.

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Song, Seulki, Hyejoo Park, Daeyoon Kim, Sheehyun Kim, Hongseok Yun, Sungyoung Lee, Youngil Koh, and Sung-Soo Yoon. "Abstract 145: Comparison of whole transcriptome sequencing immune repertoire sequencing using RNA for tumor milieu analysis." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-145.

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Song, Seulki, Hyejoo Park, Daeyoon Kim, Sheehyun Kim, Hongseok Yun, Sungyoung Lee, Youngil Koh, and Sung-Soo Yoon. "Abstract 145: Comparison of whole transcriptome sequencing immune repertoire sequencing using RNA for tumor milieu analysis." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-145.

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Duitama, Jorge, Pramod K. Srivastava, and Ion I. Mandoiu. "Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data." In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2011. http://dx.doi.org/10.1109/iccabs.2011.5729949.

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Shen, Yaoqing, Martin R. Jones, Erin Pleasance, Melika Bonakdar, Carolyn Ch'ng, Caralyn Reisle, Laura Williamson, et al. "Abstract A184: Clinical application of whole genome and transcriptome sequencing in cancer care." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; October 26-30, 2017; Philadelphia, PA. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1535-7163.targ-17-a184.

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Reports on the topic "Whole-transcriptome sequencing"

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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.

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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.
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Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.

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Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10
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