Journal articles: 'Genome-wide re-sequencing'

1

Singh, P., A. Benjak, S. Carat, M. Kai, P. Busso, C. Avanzi, A. Paniz-Mondolfi, et al. "Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3." Clinical Microbiology and Infection 20, no. 10 (October 2014): O619—O622. http://dx.doi.org/10.1111/1469-0691.12609.

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

Lin, Miaomiao, Jinbao Fang, Chungen Hu, Xiujuan Qi, Shihang Sun, Jinyong Chen, Leiming Sun, and Yunpeng Zhong. "Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing." PLOS ONE 15, no. 4 (April 10, 2020): e0219884. http://dx.doi.org/10.1371/journal.pone.0219884.

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

Yu, Xiaomin, Xujun Fu, Qinghua Yang, Hangxia Jin, Longming Zhu, and Fengjie Yuan. "Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing." Plants 11, no. 1 (December 23, 2021): 28. http://dx.doi.org/10.3390/plants11010028.

Full text

Abstract:

Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding.

APA, Harvard, Vancouver, ISO, and other styles

4

Hoggart, Clive J., John C. Whittaker, Maria De Iorio, and David J. Balding. "Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies." PLoS Genetics 4, no. 7 (July 25, 2008): e1000130. http://dx.doi.org/10.1371/journal.pgen.1000130.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

WANG, Kai, Ping-xian WU, De-juan CHEN, Jie ZHOU, Xi-di YANG, An-an JIANG, Ji-deng MA, et al. "Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs." Journal of Integrative Agriculture 20, no. 7 (July 2021): 1898–906. http://dx.doi.org/10.1016/s2095-3119(20)63488-8.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Liu, Z., H. Sun, W. Lai, M. Hu, Y. Zhang, C. Bai, J. Liu, H. Ren, F. Li, and S. Yan. "Genome‐wide re‐sequencing reveals population structure and genetic diversity of Bohai Black cattle." Animal Genetics 53, no. 1 (November 16, 2021): 133–36. http://dx.doi.org/10.1111/age.13155.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

E, Guangxin, B. ‐G Yang, W. ‐D Basang, Y. ‐B Zhu, T. ‐W An, and X. ‐L Luo. "Screening for signatures of selection of Tianzhu white yak using genome‐wide re‐sequencing." Animal Genetics 50, no. 5 (June 27, 2019): 534–38. http://dx.doi.org/10.1111/age.12817.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Marques, João P., Fernando A. Seixas, Liliana Farelo, Colin M. Callahan, Jeffrey M. Good, W. Ian Montgomery, Neil Reid, Paulo C. Alves, Pierre Boursot, and José Melo-Ferreira. "An Annotated Draft Genome of the Mountain Hare (Lepus timidus)." Genome Biology and Evolution 12, no. 1 (December 13, 2019): 3656–62. http://dx.doi.org/10.1093/gbe/evz273.

Full text

Abstract:

Abstract Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares.

APA, Harvard, Vancouver, ISO, and other styles

9

Huemer, Peter, Jean Haxaire, Kyung Min Lee, Marko Mutanen, Oleg Pekarsky, Stefano Scalercio, and László Ronkay. "Revision of the genus Hoplodrina Boursin, 1937 (Lepidoptera, Noctuidae, Xyleninae). I. Hoplodrina octogenaria (Goeze, 1781) and its sister species H. alsinides (Costantini, 1922) sp. rev. in Europe." ZooKeys 927 (April 16, 2020): 75–97. http://dx.doi.org/10.3897/zookeys.927.51142.

Full text

Abstract:

The taxonomic status of the European Hoplodrina octogenaria (Goeze, 1781) is discussed and its partly sympatric sister species, Hoplodrina alsinides (Costantini, 1922) sp. rev., is separated and re-described based on morphological and molecular taxonomic evidence. The adults and their genitalia are illustrated and DNA barcodes, as well as genome-wide single nucleotide polymorphism data collected by fractional genome sequencing (ddRAD), of the two species are provided.

APA, Harvard, Vancouver, ISO, and other styles

10

Eklöf, Helena, Carolina Bernhardsson, and Pär K. Ingvarsson. "Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies." Forests 11, no. 11 (November 10, 2020): 1185. http://dx.doi.org/10.3390/f11111185.

Full text

Abstract:

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

APA, Harvard, Vancouver, ISO, and other styles

11

Baumgarten, Sebastian, and Jessica Bryant. "Chromatin structure can introduce systematic biases in genome-wide analyses of Plasmodium falciparum." Open Research Europe 2 (September 15, 2022): 75. http://dx.doi.org/10.12688/openreseurope.14836.2.

Full text

Abstract:

Background: The maintenance, regulation, and dynamics of heterochromatin in the human malaria parasite, Plasmodium falciparum, has drawn increasing attention due to its regulatory role in mutually exclusive virulence gene expression and the silencing of key developmental regulators. The advent of genome-wide analyses such as chromatin-immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental in understanding chromatin composition; however, even in model organisms, ChIP-seq experiments are susceptible to intrinsic experimental biases arising from underlying chromatin structure. Methods: We performed a control ChIP-seq experiment, re-analyzed previously published ChIP-seq datasets and compared different analysis approaches to characterize biases of genome-wide analyses in P. falciparum. Results: We found that heterochromatic regions in input control samples used for ChIP-seq normalization are systematically underrepresented in regard to sequencing coverage across the P. falciparum genome. This underrepresentation, in combination with a non-specific or inefficient immunoprecipitation, can lead to the identification of false enrichment and peaks across these regions. We observed that such biases can also be seen at background levels in specific and efficient ChIP-seq experiments. We further report on how different read mapping approaches can also skew sequencing coverage within highly similar subtelomeric regions and virulence gene families. To ameliorate these issues, we discuss orthogonal methods that can be used to characterize bona fide chromatin-associated proteins. Conclusions: Our results highlight the impact of chromatin structure on genome-wide analyses in the parasite and the need for caution when characterizing chromatin-associated proteins and features.

APA, Harvard, Vancouver, ISO, and other styles

12

Baumgarten, Sebastian, and Jessica Bryant. "Chromatin structure can introduce systematic biases in genome-wide analyses of Plasmodium falciparum." Open Research Europe 2 (June 10, 2022): 75. http://dx.doi.org/10.12688/openreseurope.14836.1.

Full text

Abstract:

Background: The maintenance, regulation, and dynamics of heterochromatin in the human malaria parasite, Plasmodium falciparum, has drawn increasing attention due to its regulatory role in mutually exclusive virulence gene expression and the silencing of key developmental regulators. The advent of genome-wide analyses such as chromatin-immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental in understanding chromatin composition; however, even in model organisms, ChIP-seq experiments are susceptible to intrinsic experimental biases arising from underlying chromatin structure. Methods: We performed a control ChIP-seq experiment, re-analyzed previously published ChIP-seq datasets and compared different analysis approaches to characterize biases of genome-wide analyses in P. falciparum. Results: We found that heterochromatic regions in input control samples used for ChIP-seq normalization are systematically underrepresented in regard to sequencing coverage across the P. falciparum genome. This underrepresentation, in combination with a non-specific or inefficient immunoprecipitation, can lead to the identification of false enrichment and peaks across these regions. We observed that such biases can also be seen at background levels in specific and efficient ChIP-seq experiments. We further report on how different read mapping approaches can also skew sequencing coverage within highly similar subtelomeric regions and virulence gene families. To ameliorate these issues, we discuss orthogonal methods that can be used to characterize bona fide chromatin-associated proteins. Conclusions: Our results highlight the impact of chromatin structure on genome-wide analyses in the parasite and the need for caution when characterizing chromatin-associated proteins and features.

APA, Harvard, Vancouver, ISO, and other styles

13

Eun, Chang-Ho, and In-Jung Kim. "Genome-wide DNA polymorphisms of Citrus unshiu Marc. cv. Miyagawa-wase cultivated in different regions based on whole-genome re-sequencing." Plant Biotechnology Reports 15, no. 4 (August 2021): 551–59. http://dx.doi.org/10.1007/s11816-021-00696-z.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

Fu, Chong-Yun, Wu-Ge Liu, Di-Lin Liu, Ji-Hua Li, Man-Shan Zhu, Yi-Long Liao, Zhen-Rong Liu, Xue-Qin Zeng, and Feng Wang. "Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing." Genome 59, no. 3 (March 2016): 197–207. http://dx.doi.org/10.1139/gen-2015-0101.

Full text

Abstract:

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica ‘Nipponbare’) reference genome. A total of 2 758 740 polymorphic sites including 2 408 845 SNPs and 349 895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961 791 SNPs and 46 640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

APA, Harvard, Vancouver, ISO, and other styles

15

Coetzee, Beatrix, Elma Carstens, Megan Dewdney, Paul H. Fourie, and Aletta E. Bester-van der Merwe. "Extending the knowledge of Phyllosticta citricarpa population structure in USA with re-sequencing and genome wide analysis." Physiological and Molecular Plant Pathology 113 (January 2021): 101591. http://dx.doi.org/10.1016/j.pmpp.2020.101591.

Full text

APA, Harvard, Vancouver, ISO, and other styles

16

Modrek, Aram, Catherine Do, Zeyan Zhang, Yingwen Deng, Jerome Karp, Ravesanker Ezhilarasan, Belen Valor, et al. "EPCO-19. ADAPTIVE RESPONSES TO GENOME-WIDE DNA DAMAGE RESULT IN TOPOLOGIC GENOME REORGANIZATION IN GLIOBLASTOMA." Neuro-Oncology 24, Supplement_7 (November 1, 2022): vii119—vii120. http://dx.doi.org/10.1093/neuonc/noac209.454.

Full text

Abstract:

Abstract In glioblastoma, treatment with radiation and chemotherapy leads to DNA-damage and most DNA breaks are faithfully repaired, but the impact on the epigenome is largely unknown. Using newly developed tools to enable these studies, we hypothesize that genome-wide DNA damage leads to local alterations in DNA-methylation, genome organization, and results in persistent gene-expression alterations near sites of repaired damage. We use patient-derived human glioblastoma stem-like cells (GSCs) as a model. DNA breaks are induced using (i) irradiation or (ii) a novel “multi-cut” CRISPR-Cas9 DNA break system followed by multi-omic profiling. With radiation, we find significant and wide-spread alterations in DNA-methylation after treating multiple glioblastoma cultures. However, it is challenging to study local alterations around sites of radiation induced damage because breaks are introduced at different sites in each cell, resulting in stochastic DNA methylation alterations. To circumvent this issue, we developed a multi-cut CRISPR-Cas9 DNA break system that targets 142 or 483 pre-defined loci. Induction of pre-mapped genome-wide cuts reproduces a similar level of toxicity as standard doses of radiation. To assess repair efficiency and confirm induction of breaks, we performed targeted sequencing of the 142 or 483 sites to allow for high coverage sequencing. To understand how DNA damage may lead to regional epigenetic and 3D chromatin organization changes, we performed HiC, Methylation-seq, ChIP-seq of the chromatin organizing factor CTCF and enhancer marker H3K27ac, as well as RNA-seq, before and after cut induction. Our findings show significant mega-base scale alterations in chromatin contacts centered around cut sites, enrichment of DNA methylation alterations at regulatory elements and altered gene-expression. The findings here provide a mechanistic view of the interplay between genome-wide DNA damage, DNA methylation and genome re-organization, and have wide ranging implications for the effect of DNA damage on the epigenome in glioblastoma.

APA, Harvard, Vancouver, ISO, and other styles

17

Hu, Jihong, Songtao Gui, Zhixuan Zhu, Xiaolei Wang, Weidong Ke, and Yi Ding. "Genome-Wide Identification of SSR and SNP Markers Based on Whole-Genome Re-Sequencing of a Thailand Wild Sacred Lotus (Nelumbo nucifera)." PLOS ONE 10, no. 11 (November 25, 2015): e0143765. http://dx.doi.org/10.1371/journal.pone.0143765.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Ratnaparkhe, Milind Balkrishna, Niharika Marmat, Giriraj Kumawat, Maranna Shivakumar, Viraj Gangadhar Kamble, Vennampally Nataraj, Shunmugiah Veluchamy Ramesh, et al. "Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance." Current Genomics 21, no. 7 (October 22, 2020): 504–11. http://dx.doi.org/10.2174/1389202921999200601142258.

Full text

Abstract:

Background: In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism. Methods: A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes. Results: Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred. by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus. Conclusion: The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.

APA, Harvard, Vancouver, ISO, and other styles

19

ZHAO, Qing-Ying, Rui-Juan ZHANG, Rui-Liang WANG, Jian-Hua GAO, Yuan-Huai HAN, Zhi-Rong YANG, and Xing-Chun WANG. "Genome-wide Identification of Molecular Markers Based on Genomic Re-sequencing of Foxtail Millet Elite Cultivar Jingu 21." Acta Agronomica Sinica 44, no. 5 (2018): 686. http://dx.doi.org/10.3724/sp.j.1006.2018.00686.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Xiong, Yang, Dan-Yang Wang, Wenjie Guo, Gaorui Gong, Zhen-Xia Chen, Qin Tang, and Jie Mei. "Sexually Dimorphic Gene Expression in X and Y Sperms Instructs Sexual Dimorphism of Embryonic Genome Activation in Yellow Catfish (Pelteobagrus fulvidraco)." Biology 11, no. 12 (December 14, 2022): 1818. http://dx.doi.org/10.3390/biology11121818.

Full text

Abstract:

Paternal factors play an important role in embryonic morphogenesis and contribute to sexual dimorphism in development. To assess the effect of paternal DNA on sexual dimorphism of embryonic genome activation, we compared X and Y sperm and different sexes of embryos before sex determination. Through transcriptome sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS) of X and Y sperm, we found a big proportion of upregulated genes in Y sperm, supported by the observation that genome-wide DNA methylation level is slightly lower than in X sperm. Cytokine–cytokine receptor interaction, TGF-beta, and toll-like receptor pathways play important roles in spermatogenesis. Through whole-genome re-sequencing (WGRS) of parental fish and RNA-seq of five early embryonic stages, we found the low-blastocyst time point is a key to maternal transcriptome degradation and zygotic genome activation. Generally, sexual differences emerged from the bud stage. Moreover, through integrated analysis of paternal SNPs and gene expression, we evaluated the influence of paternal inheritance on sexual dimorphism of genome activation. Besides, we screened out gata6 and ddx5 as potential instructors for early sex determination and gonad development in yellow catfish. This work is meaningful for revealing the molecular mechanisms of sex determination and sexual dimorphism of fish species.

APA, Harvard, Vancouver, ISO, and other styles

21

Trucchi, Emiliano, Paolo Gratton, Jason D. Whittington, Robin Cristofari, Yvon Le Maho, Nils Chr Stenseth, and Céline Le Bohec. "King penguin demography since the last glaciation inferred from genome-wide data." Proceedings of the Royal Society B: Biological Sciences 281, no. 1787 (July 22, 2014): 20140528. http://dx.doi.org/10.1098/rspb.2014.0528.

Full text

Abstract:

How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum ( ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus . Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition.

APA, Harvard, Vancouver, ISO, and other styles

22

Buller, Nicky, and Sam Hair. "Identification of bacteria from aquatic animals." Microbiology Australia 37, no. 3 (2016): 129. http://dx.doi.org/10.1071/ma16044.

Full text

Abstract:

A wide range of aquatic animal species are cultured for human consumption, the fashion industry, research purposes or re-stocking natural populations. Each host species may be colonised by bacterial saprophytes or infected with pathogens that have specific growth requirements encompassing temperature, salinity, trace elements or ions. To ensure successful culture and identification of potential pathogens, the microbiologist must have in-depth knowledge of these growth requirements and access to the appropriate resources. Identification techniques include traditional culture and biochemical identification methods modified to take into account any growth requirements, identification using mass spectrometry, detection of nucleic acids, sequencing 16S rRNA or specific genes, and whole genome sequencing.

APA, Harvard, Vancouver, ISO, and other styles

23

Shirasawa, K., H. Fukuoka, H. Matsunaga, Y. Kobayashi, I. Kobayashi, H. Hirakawa, S. Isobe, and S. Tabata. "Genome-Wide Association Studies Using Single Nucleotide Polymorphism Markers Developed by Re-Sequencing of the Genomes of Cultivated Tomato." DNA Research 20, no. 6 (July 31, 2013): 593–603. http://dx.doi.org/10.1093/dnares/dst033.

Full text

APA, Harvard, Vancouver, ISO, and other styles

24

Ejigu, Girum Fitihamlak, and Jaehee Jung. "Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing." Biology 9, no. 9 (September 18, 2020): 295. http://dx.doi.org/10.3390/biology9090295.

Full text

Abstract:

Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.

APA, Harvard, Vancouver, ISO, and other styles

25

Xiao, Shijun, Panpan Wang, Linsong Dong, Yaguang Zhang, Zhaofang Han, Qiurong Wang, and Zhiyong Wang. "Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea." PeerJ 4 (December 21, 2016): e2664. http://dx.doi.org/10.7717/peerj.2664.

Full text

Abstract:

Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS) provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used anEcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such asAPOB,CRATandOSBPL10. Notably,PPT2Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified thatEcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.

APA, Harvard, Vancouver, ISO, and other styles

26

Khan, Sawar, Ayesha Nisar, Jianqi Yuan, Xiaoping Luo, Xueqin Dou, Fei Liu, Xiaochao Zhao, et al. "A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus." Genes 11, no. 4 (March 28, 2020): 367. http://dx.doi.org/10.3390/genes11040367.

Full text

Abstract:

The most important and broad-spectrum drug used to control the parasitic worms to date is ivermectin (IVM). Resistance against IVM has emerged in parasites, and preserving its efficacy is now becoming a serious issue. The parasitic nematode Haemonchus contortus (Rudolphi, 1803) is economically an important parasite of small ruminants across the globe, which has a successful track record in IVM resistance. There are growing evidences regarding the multigenic nature of IVM resistance, and although some genes have been proposed as candidates of IVM resistance using lower magnification of genome, the genetic basis of IVM resistance still remains poorly resolved. Using the full magnification of genome, we herein applied a population genomics approach to characterize genome-wide signatures of selection among pooled worms from two susceptible and six ivermectin-resistant isolates of H. contortus, and revealed candidate genes under selection in relation to IVM resistance. These candidates also included a previously known IVM-resistance-associated candidate gene HCON_00148840, glc-3. Finally, an RNA-interference-based functional validation assay revealed the HCON_00143950 as IVM-tolerance-associated gene in H. contortus. The possible role of this gene in IVM resistance could be detoxification of xenobiotic in phase I of xenobiotic metabolism. The results of this study further enhance our understanding on the IVM resistance and continue to provide further evidence in favor of multigenic nature of IVM resistance.

APA, Harvard, Vancouver, ISO, and other styles

27

Huang, Zhenyu, Fei Shen, Yuling Chen, Ke Cao, and Lirong Wang. "Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study." Plants 10, no. 2 (January 27, 2021): 242. http://dx.doi.org/10.3390/plants10020242.

Full text

Abstract:

Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key genes related to peach pollen fertility trait. The significant association peak was detected at Chr.06: 2,116,368 bp, which was in accordance with the previous genetic mapping results, but displayed largely improved precision, allowing for the identification of nine candidate genes. Among these candidates, gene PpABCG26, encoding an ATP-binding cassette G (ABCG) transporter and harboring the most significantly associated SNP (Single Nucleotide Polymorphism) marker in its coding region, was hypothesized to control peach pollen fertility/sterility based on the results of gene function comparison, gene relative expression, and nucleotide sequence analysis. The obtained results will help us to understand the genetic basis of peach pollen fertility trait, and to discover applicable markers for pre-selection in peach.

APA, Harvard, Vancouver, ISO, and other styles

28

Ghosh Dasgupta, Modhumita, Muneera Parveen Abdul Bari, Senthilkumar Shanmugavel, Veeramuthu Dharanishanthi, Muthusamy Muthupandi, Naveen Kumar, Shakti Singh Chauhan, et al. "Targeted re-sequencing and genome-wide association analysis for wood property traits in breeding population of Eucalyptus tereticornis × E. grandis." Genomics 113, no. 6 (November 2021): 4276–92. http://dx.doi.org/10.1016/j.ygeno.2021.11.013.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Moutsianas, L., and A. P. Morris. "Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits." Briefings in Functional Genomics 13, no. 5 (June 10, 2014): 362–70. http://dx.doi.org/10.1093/bfgp/elu012.

Full text

APA, Harvard, Vancouver, ISO, and other styles

30

Yuan, Huanran, Weilong Yang, Jianing Zou, Mingxing Cheng, Fengfeng Fan, Ting Liang, Yajie Yu, Ronghua Qiu, Shaoqing Li, and Jun Hu. "InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice (Oryza sativa L.)." Agriculture 11, no. 7 (July 11, 2021): 655. http://dx.doi.org/10.3390/agriculture11070655.

Full text

Abstract:

A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms in gene mapping, analysing genetic diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, a re-sequencing project, discovered millions of genome-wide InDels. We found that the proportion of >50-bp long InDels (699,475) of the total (1,248,503) is 56.02%. The number of InDels on each chromosome was consistent with the corresponding chromosome length. The maximum InDels were on chromosome 1 (78,935), and the minimum InDels were on chromosome 9 (41,752), with an average density of 1.87 InDels/kb (range: 1.50–2.36 InDels/kb). Furthermore, 96 InDels of about 3.98 Mb/InDel were selected to detect the polymorphism. The results exhibited ideal performance in 2% agarose gel electrophoresis. Phylogenetic analysis exhibited that InDel markers had excellent polymorphisms between rice varieties of japonica and indica, and varieties could be classified based on the statistical results of their polymorphisms. The InDel markers could be applied to identify the recombinant inbred lines in a population. These results reveal that the high-density long InDel markers could help us examine the functional diversity, species variation, and map-based cloning.

APA, Harvard, Vancouver, ISO, and other styles

31

van Eif, Vincent W. W., Stephanie I. Protze, Fernanda M. Bosada, Xuefei Yuan, Tanvi Sinha, Karel van Duijvenboden, Auriane C. Ernault, et al. "Genome-Wide Analysis Identifies an Essential Human TBX3 Pacemaker Enhancer." Circulation Research 127, no. 12 (December 4, 2020): 1522–35. http://dx.doi.org/10.1161/circresaha.120.317054.

Full text

Abstract:

Rationale: The development and function of the pacemaker cardiomyocytes of the sinoatrial node (SAN), the leading pacemaker of the heart, are tightly controlled by a conserved network of transcription factors, including TBX3 (T-box transcription factor 3), ISL1 (ISL LIM homeobox 1), and SHOX2 (short stature homeobox 2). Yet, the regulatory DNA elements (REs) controlling target gene expression in the SAN pacemaker cells have remained undefined. Objective: Identification of the regulatory landscape of human SAN-like pacemaker cells and functional assessment of SAN-specific REs potentially involved in pacemaker cell gene regulation. Methods and Results: We performed Assay for Transposase-Accessible Chromatin using sequencing on human pluripotent stem cell–derived SAN-like pacemaker cells and ventricle-like cells and identified thousands of putative REs specific for either human cell type. We validated pacemaker cell–specific elements in the SHOX2 and TBX3 loci. CRISPR-mediated homozygous deletion of the mouse ortholog of a noncoding region with candidate pacemaker-specific REs in the SHOX2 locus resulted in selective loss of Shox2 expression from the developing SAN and embryonic lethality. Putative pacemaker-specific REs were identified up to 1 Mbp upstream of TBX3 in a region close to MED13L harboring variants associated with heart rate recovery after exercise. The orthologous region was deleted in mice, which resulted in selective loss of expression of Tbx3 from the SAN and (cardiac) ganglia and in neonatal lethality. Expression of Tbx3 was maintained in other tissues including the atrioventricular conduction system, lungs, and liver. Heterozygous adult mice showed increased SAN recovery times after pacing. The human REs harboring the associated variants robustly drove expression in the SAN of transgenic mouse embryos. Conclusions: We provided a genome-wide collection of candidate human pacemaker-specific REs, including the loci of SHOX2 , TBX3 , and ISL1 , and identified a link between human genetic variants influencing heart rate recovery after exercise and a variant RE with highly conserved function, driving SAN expression of TBX3 .

APA, Harvard, Vancouver, ISO, and other styles

32

Cahill, Nicola, Meena Kanduri, Hanna Göransson, Anders Isaksson, Camilla Enström, Fergus Ryan, and Richard Rosenquist. "Genome-Wide Methylation Arrays Reveal Distinct Methylation Profiles in Prognostic Subsets of Chronic Lymphocytic Leukemia." Blood 114, no. 22 (November 20, 2009): 364. http://dx.doi.org/10.1182/blood.v114.22.364.364.

Full text

Abstract:

Abstract Abstract 364 Introduction: Aberrant DNA methylation has been shown to play a strong role in tumorogenesis, where genome-wide hypomethylation and regional hypermethylation of tumor suppressor gene (TGS) promoters are characteristic hallmarks of many cancers. In chronic lymphocytic leukemia (CLL), the epigenetic mechanism of gene regulation has thus far received limited attention, although promoter methylation and transcriptional silencing has been shown for certain individual genes, for example, DAPK1, ZAP70 and PEG10. To date, only the ‘Restriction Landmark Genomic Scanning' technique has been performed to assess the genome-wide methylation status in CLL. However, this technique spans only 3000 CpG islands and does not give a full coverage of the genome. Patients and methods: Here, we analyzed the global methylation profiles in CLL by applying high-resolution genome-wide methylation arrays from Illumina that cover 28,000 CpG sites, spanning 14,000 genes. Specifically, 23 CLL samples belonging to the immunoglobulin heavy-chain variable (IGHV) mutated (favorable prognostic) and IGHV unmutated/IGHV3-21 (poor-prognostic) subsets were analysed. The raw data was processed using the BeadStudio software followed by bioinformatic analysis where the arcsin transformed data was used in a moderated t-test to find differentially methylated genes. Only genes with a large absolute difference between the groups were included for further analysis. Methylation-specific PCR (MSP-PCR) and realtime-PCR (RQ-PCR) were performed on a selection of genes to confirm the array data. Additionally, bi-sulfite sequencing was employed on selected genes to confirm the degree of methylation. Moreover, CLL samples were treated with the DNA methyl transferase inhibitor 5-aza-2'-deoxycytidine combined with and without the histone deacetylase inhibitor (HDAC) trichostatin A to induce re-expression of selected methylated genes Results: Overall, we observed significant differences in methylation patterns between the CLL subgroups. Specifically, we identified TSGs that were preferentially methylated in the IGHV unmutated (7 genes, e.g. VHL, ABI3) and IGHV3-21(1 gene, SLC22A18) subgroups. We also identified 10 unmethylated and hence potentially expressed genes shown to be involved in activation of proliferative pathways such as the NFkB pathway (e.g. ADORA3), and the MAP/ERK kinase pathway (e.g. FABP7) in the IGHV unmutated and IGHV3-21 subgroups. In contrast, these latter genes were silenced by methylation in IGHV mutated patients. The methylation status was verified for 4 genes (BCL10, PRF1, ADORA3 and IGSF4) by MSP-PCR and the expression status of 7 genes (BCL10, PRF1, ADORA3, IGSF4, NGFR, ABI3 and VHL) was confirmed using RQ-PCR. Furthermore, bi-sulfite sequencing confirmed the degree of methylation for 2 methylated TSGs (VHL and ABI3) in unmutated CLL samples. Finally, the significance of DNA methylation in regulating gene promoters was shown by re-inducing 3 methylated TSGs ( VHL, ABI3 and IGSF4) in IGHV unmutated samples using the methyl-inhibitor 5-aza-2'-deoxycytidine. Conclusion: Taken together, our data for the first time reveals differences in global methylation profiles between prognostic subsets of CLL, which may unfold important epigenetic silencing mechanisms involved in CLL pathogenesis. Specific inhibition of expression of unmethylated genes involved in facilitating tumorogenesis and re-expression of methylated tumor suppressor genes within the poor-prognostic CLL subgroups may represent potential new drug therapy targets. Disclosures: No relevant conflicts of interest to declare.

APA, Harvard, Vancouver, ISO, and other styles

33

Gabriel, Kristianne Arielle, Maria Rejane Nepacina, Francis Tablizo, Carlo Lapid, Mark Lenczner Mendoza, Daniella Jean Pamulaklakin, Jobeth Domingo, et al. "Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design." F1000Research 10 (May 7, 2021): 360. http://dx.doi.org/10.12688/f1000research.52141.1.

Full text

Abstract:

Reduced representation sequencing is a practical approach for obtaining genetic variations from a random subsample of the genome. RADseq (Restriction Site-Associated DNA Sequencing), as one of the more popular reduced representation approaches, is currently being used in a wide array of applications including marker development, phylogenetics, and population genomics. A crucial step in designing a RADseq experiment is the selection of one or a pair of restriction enzymes (RE) that will result in sufficient density of loci to meet the objectives of the study, which is not straightforward because of difficulties in obtaining a standard set of REs that can generally be applied to RADseq experimental designs. Here we present RApyDS, a simulation tool that provides users with evaluation metrics to aid in choosing suitable REs based on their target RADseq design. RApyDS can perform simulations for single- or double-digest RADseq, preferably with a supplied reference genome. The tool outputs an overview page, electrophoresis visualization, mapping of restriction cut sites, and RAD loci density across the genome. If supplied with an annotation file, the program can also output evaluation metrics for a specified genomic feature. The tool is currently available at https://github.com/pgcbioinfo/rapyds.

APA, Harvard, Vancouver, ISO, and other styles

34

Chen, Long, Jennie E. Pryce, Ben J. Hayes, and Hans D. Daetwyler. "Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle." Animals 11, no. 2 (February 19, 2021): 541. http://dx.doi.org/10.3390/ani11020541.

Full text

Abstract:

Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individuals genotyped with single-nucleotide polymorphism (SNP) panels without the expense of sequencing them. In this study, we generated 24,908 high-quality SVs in a total of 478 whole-genome sequenced Holstein and Jersey cattle. We imputed 4489 SVs with R2 > 0.5 into 35,568 Holstein and Jersey dairy cattle with 578,999 SNPs with two pipelines, FImpute and Eagle2.3-Minimac3. Genome-wide association studies for production, fertility and overall type with these 4489 SVs revealed four significant SVs, of which two were highly linked to significant SNP. We also estimated the variance components for SNP and SV models for these traits using genomic best linear unbiased prediction (GBLUP). Furthermore, we assessed the effect on genomic prediction accuracy of adding SVs to GBLUP models. The estimated percentage of genetic variance captured by SVs for production traits was up to 4.57% for milk yield in bulls and 3.53% for protein yield in cows. Finally, no consistent increase in genomic prediction accuracy was observed when including SVs in GBLUP.

APA, Harvard, Vancouver, ISO, and other styles

35

Narum, Shawn R., Alex Di Genova, Steven J. Micheletti, and Alejandro Maass. "Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon." Proceedings of the Royal Society B: Biological Sciences 285, no. 1883 (July 18, 2018): 20180935. http://dx.doi.org/10.1098/rspb.2018.0935.

Full text

Abstract:

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon ( Oncorhynchus tshawytscha ; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.

APA, Harvard, Vancouver, ISO, and other styles

36

Singh, Nisha, Hukam C. Rawal, Ulavappa B. Angadi, Tilak Raj Sharma, Nagendra Kumar Singh, and Tapan Kumar Mondal. "A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz)." Bioinformatics 38, no. 2 (October 2, 2021): 318–24. http://dx.doi.org/10.1093/bioinformatics/btab690.

Full text

Abstract:

Abstract Motivation Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery. Results In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of ∼0.31× per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties. Supplementary information Supplementary data are available at Bioinformatics online.

APA, Harvard, Vancouver, ISO, and other styles

37

Geibel, Johannes, Christian Reimer, Steffen Weigend, Annett Weigend, Torsten Pook, and Henner Simianer. "How array design creates SNP ascertainment bias." PLOS ONE 16, no. 3 (March 30, 2021): e0245178. http://dx.doi.org/10.1371/journal.pone.0245178.

Full text

Abstract:

Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™Genome-Wide Chicken Arrayin silicoand evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.

APA, Harvard, Vancouver, ISO, and other styles

38

Milchevskaya, Vladislava, Grischa Tödt, and Toby James Gibson. "A Tool to Build Up-To-Date Gene Annotations for Affymetrix Microarrays." Genomics and Computational Biology 3, no. 2 (January 31, 2017): 38. http://dx.doi.org/10.18547/gcb.2017.vol3.iss2.e38.

Full text

Abstract:

Genome-wide expression profiling and genotyping is widely applied in functional genomics research, ranging from stem cell studies to cancer, in drug response studies, and in clinical diagnostics. The Affymetrix GeneChip microarrays represent the most popular platform for such assays. Nevertheless, due to rapid and continuous improvement of the knowledge about the genome, the definition of many of the genes and transcripts change, and new genes are discovered. Thus the original probe information is out-dated for a number of Affymetrix platforms, and needs to be re-defined. It has been demonstrated, that accurate probe set definition improves both coverage of the gene expression analysis and its statistical power. Therefore we developed a method that incorporates the most recent genome annotations into the annotation of the microarray probe sets, using tools from the next generation sequencing. Additionally our method allows to quickly build project specific gene annotation models, as well as for comparison of microarray to RNAseq data.

APA, Harvard, Vancouver, ISO, and other styles

39

MARGOS, GABRIELE, SANTIAGO CASTILLO-RAMÍREZ, and ANNE GATEWOOD HOEN. "Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistantStaphylococcus aureus." Parasitology 139, no. 14 (May 23, 2012): 1952–65. http://dx.doi.org/10.1017/s0031182012000741.

Full text

Abstract:

SUMMARYMultilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have revolutionized understanding the global epidemiology of many medically relevant bacteria utilizing a number, mostly seven, of housekeeping genes. A more recent introduction, single nucleotide polymorphisms (SNPs), constitutes an even more powerful tool for bacterial typing, population genetic studies and phylogeography. The introduction of massive parallel sequencing has made genome re-sequencing and SNP discovery more economical for investigations of microbial organisms. In this paper we review phylogeographic studies on Lyme borreliosis (LB)-group spirochetes and methicillin-resistantStaphylococcus aureus(MRSA). Members of the LB-group spirochetes are tick-transmitted zoonotic bacteria that have many hosts and differ in their degree of host specialism, constituting a highly complex system. MRSA is a directly transmitted pathogen that may be acquired by contact with infected people, animals or MRSA-contaminated objects. For the LB-group spirochetes, MLSA has proved a powerful tool for species assignment and phylogeographic investigations while forS. aureus, genome-wide SNP data have been used to study the very short-term evolution of two important MRSA lineages, ST239 and ST225. These data are detailed in this review.

APA, Harvard, Vancouver, ISO, and other styles

40

Ni, Xiaopeng, Song Xue, Shahid Iqbal, Wanxu Wang, Zhaojun Ni, Muhammad Khalil-ur-Rehman, and Zhihong Gao. "Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)." PeerJ 6 (May 4, 2018): e4625. http://dx.doi.org/10.7717/peerj.4625.

Full text

Abstract:

The red-skinned fruit of Japanese apricot (Prunus mumeSieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL,F3HandUFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1,RT1,UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.

APA, Harvard, Vancouver, ISO, and other styles

41

Loera-Sánchez, Miguel, Bruno Studer, and Roland Kölliker. "DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications." Agronomy 9, no. 12 (December 12, 2019): 881. http://dx.doi.org/10.3390/agronomy9120881.

Full text

Abstract:

Grasslands are wide-spread, multi-species ecosystems that provide many valuable services. Plant genetic diversity (i.e., the diversity within species) is closely linked to ecosystem functioning in grasslands and constitutes an important reservoir of genetic resources that can be used to breed improved cultivars of forage grass and legume species. Assessing genetic diversity in grassland plant species is demanding due to the large number of different species and the level of resolution needed. However, recent methodological advances could help in tackling this challenge at a larger scale. In this review, we outline the methods that can be used to measure genetic diversity in plants, highlighting their strengths and limitations for genetic diversity assessments of grassland plant species, with a special focus on forage plants. Such methods can be categorized into DNA fragment, hybridization array, and high-throughput sequencing (HTS) methods, and they differ in terms of resolution, throughput, and multiplexing potential. Special attention is given to HTS approaches (i.e., plastid genome skimming, whole genome re-sequencing, reduced representation libraries, sequence capture, and amplicon sequencing), because they enable unprecedented large-scale assessments of genetic diversity in non-model organisms with complex genomes, such as forage grasses and legumes. As no single method may be suited for all kinds of purposes, we also provide practical perspectives for genetic diversity analyses in forage breeding and genetic resource conservation efforts.

APA, Harvard, Vancouver, ISO, and other styles

42

Tsai, Ming-Hsin, Yen-Yi Liu, Von-Wun Soo, and Chih-Chieh Chen. "A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy." Microorganisms 7, no. 6 (June 3, 2019): 161. http://dx.doi.org/10.3390/microorganisms7060161.

Full text

Abstract:

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

APA, Harvard, Vancouver, ISO, and other styles

43

Wang, Yali, and Yi Li. "Population Genetics and Development of a Core Collection from Elite Germplasms of Xanthoceras sorbifolium Based on Genome-Wide SNPs." Forests 13, no. 2 (February 18, 2022): 338. http://dx.doi.org/10.3390/f13020338.

Full text

Abstract:

Xanthoceras sorbifolium is one of the most important species of woody oil. In this study, whole genome re-sequencing of 119 X. sorbifolium germplasms was conducted and, after filtering, 105,685,557 high-quality SNPs were identified, which were used to perform population genetics and core collection development analyses. The results from the phylogenetic, population structure, and principal component analyses showed a high level of agreement, with 119 germplasms being classified into three main groups. The germplasms were not completely classified based on their geographical origins and flower colors; furthermore, the genetic backgrounds of these germplasms were complex and diverse. The average polymorphsim information content (PIC) values for the three inferred groups clustered by structure analysis and the six classified color groups were 0.2445 and 0.2628, respectively, indicating a low to medium informative degree of genetic diversity. Moreover, a core collection containing 29.4% (35) out of the 119 X. sorbifolium germplasms was established. Our results revealed the genetic diversity and structure of X. sorbifolium germplasms, and the development of a core collection will be useful for the efficient improvement of breeding programs and genome-wide association studies.

APA, Harvard, Vancouver, ISO, and other styles

44

Liu, Wen, Fozia Ghouri, Hang Yu, Xiang Li, Shuhong Yu, Muhammad Qasim Shahid, and Xiangdong Liu. "Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes." PLOS ONE 12, no. 7 (July 11, 2017): e0180662. http://dx.doi.org/10.1371/journal.pone.0180662.

Full text

APA, Harvard, Vancouver, ISO, and other styles

45

Bai, Hui, Yinghao Cao, Jianzhang Quan, Li Dong, Zhiyong Li, Yanbin Zhu, Lihuang Zhu, Zhiping Dong, and Dayong Li. "Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet." PLoS ONE 8, no. 9 (September 10, 2013): e73514. http://dx.doi.org/10.1371/journal.pone.0073514.

Full text

APA, Harvard, Vancouver, ISO, and other styles

46

Yu, Jian, Pengju Zhao, Xianrui Zheng, Lei Zhou, Chuduan Wang, and Jian-Feng Liu. "Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality." G3: Genes|Genomes|Genetics 10, no. 10 (August 28, 2020): 3765–73. http://dx.doi.org/10.1534/g3.120.401628.

Full text

Abstract:

With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (di, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc’s excellent phenotypic traits.

APA, Harvard, Vancouver, ISO, and other styles

47

Luo, Huaiyong, Xiaojie Wang, Gangming Zhan, Guorong Wei, Xinli Zhou, Jing Zhao, Lili Huang, and Zhensheng Kang. "Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus." PLOS ONE 10, no. 6 (June 12, 2015): e0130362. http://dx.doi.org/10.1371/journal.pone.0130362.

Full text

APA, Harvard, Vancouver, ISO, and other styles

48

Whiting, James R., Josephine R. Paris, Paul J. Parsons, Sophie Matthews, Yuridia Reynoso, Kimberly A. Hughes, David Reznick, and Bonnie A. Fraser. "On the genetic architecture of rapidly adapting and convergent life history traits in guppies." Heredity 128, no. 4 (March 8, 2022): 250–60. http://dx.doi.org/10.1038/s41437-022-00512-6.

Full text

Abstract:

AbstractThe genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL crosses to examine the genetic basis of seven (five female, two male) guppy life history phenotypes and discuss how these genetic architectures may facilitate or constrain rapid adaptation and convergence. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many loci of small-effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid, repeatable phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but subsequent genetic redundancy may limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent analyses of wild guppies.

APA, Harvard, Vancouver, ISO, and other styles

49

Qin, Ling, Erying Chen, Feifei Li, Xiao Yu, Zhenyu Liu, Yanbing Yang, Runfeng Wang, et al. "Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)." International Journal of Molecular Sciences 21, no. 22 (November 12, 2020): 8520. http://dx.doi.org/10.3390/ijms21228520.

Full text

Abstract:

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

APA, Harvard, Vancouver, ISO, and other styles

50

She, Kuijun, Wenqiu Pan, Ying Yan, Tingrui Shi, Yingqi Chu, Yue Cheng, Bo Ma, and Weining Song. "Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley (Hordeum vulgare L.)." International Journal of Molecular Sciences 23, no. 21 (October 27, 2022): 13027. http://dx.doi.org/10.3390/ijms232113027.

Full text

Abstract:

The hyperosmolality-gated calcium-permeable channel gene family (OSCA) is one kind of conserved osmosensors, playing a crucial role in maintaining ion and water homeostasis and protecting cellular stability from the damage of hypertonic stress. Although it has been systematically characterized in diverse plants, it is necessary to explore the role of the OSCA family in barley, especially its importance in regulating abiotic stress response. In this study, a total of 13 OSCA genes (HvOSCAs) were identified in barley through an in silico genome search method, which were clustered into 4 clades based on phylogenetic relationships with members in the same clade showing similar protein structures and conserved motif compositions. These HvOSCAs had many cis-regulatory elements related to various abiotic stress, such as MBS and ARE, indicating their potential roles in abiotic stress regulation. Furthermore, their expression patterns were systematically detected under diverse stresses using RNA-seq data and qRT-PCR methods. All of these 13 HvOSCAs were significantly induced by drought, cold, salt and ABA treatment, demonstrating their functions in osmotic regulation. Finally, the genetic variations of the HvOSCAs were investigated using the re-sequencing data, and their nucleotide diversity in wild barley and landrace populations were 0.4966 × 10−3 and 0.391 × 10−3, respectively, indicating that a genetic bottleneck has occurred in the OSCA family during the barley evolution process. This study evaluated the genomic organization, evolutionary relationship and genetic expression of the OSCA family in barley, which not only provides potential candidates for further functional genomic study, but also contributes to genetically improving stress tolerance in barley and other crops.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Genome-wide re-sequencing'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles