Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Dong, Yang; Xie, Min; Jiang, Yu; Xiao, Nianqing; Du, Xiaoyong; Zhang, Wenguang; Tosser‐Klopp, Gwenola; Wang, Jinhuan; Yang, Shuang; Liang, Jie; Chen, Wenbin; Chen, Jing; Zeng, Peng; Hou, Yong; Bian, Chao; Pan, Shengkai; Li, Yuxiang; Liu, Xin; Wang, Wenliang; Servin, Bertrand; Sayre, Brian; Zhu, Bin; Sweeney, Deacon; Moore, Rod; Nie, Wei; Shen, Yongyi; Zhao, Ruoping; Zhang, Guojie; Li, Jinquan; Faraut, Thomas; Womack, James E.; Zhang, Yaping; Kijas, James W.; Cockett, Noelle E.; Xu, Xun; Zhao, Shuhong; Wang, Jun; Wang, Wen

doi:10.1038/nbt.2478

Cited by 447 publications

(449 citation statements)

References 63 publications

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“…A high degree of similarity in full genome sequences (Dong et al, 2013) and a significant overlap in regions harboring copy number variations (Fontanesi et al, 2011) has been observed among cattle, sheep and goats, indicating minor genomic differences since their divergence from a common ancestor around 19-40 million years ago. If one therefore assumes that goats and sheep share a common genome architecture associated with similar phenotypes, then the expectation is that they should share consensus signatures of natural selection when exposed to a common environment.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, similar efforts at developing and refining the goat genome have lagged behind, but recent years have witnessed a slow increase in gene mapping data since the first genetic and cytogenetic maps were produced (Vaiman et al, 1996;Schibler et al, 1998) and 550 loci have been mapped to the goat genome using linkage maps of low resolution (Schibler et al, 2009). The initial release of the goat genome sequence (Dong et al, 2013) was based entirely on short-read de novo sequencing that yielded an~2.66 Gb assembly with a contig N50 length of 3.06 Mb. Du et al (2014) have attempted to improve the quality of this genome using additional illumina new-generation shortread sequences and the optical mapping technology of large DNA molecules that have permitted the assembly of 349 super-scaffolds with N50 length of 18.2 Mb.…”

Section: Discussionmentioning

confidence: 99%

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Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

et al. 2015

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Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

et al. 2015

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“…High molecular weight DNA was obtained from Chinese hamster tissues. Whole genome shotgun, single-molecule restriction maps were generated using the automated Argus system (OpGen Inc., Maryland, USA), based on the optical mapping technology 51,52 . Individual DNA molecules were deposited onto silane-derivatized glass surfaces in MapCards (OpGen Inc., MD, USA) and digested by BamHI enzyme.…”

Section: Methodsmentioning

confidence: 99%

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Lewis¹,

et al. 2013

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Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has been well documented, a systematic, nucleotide-resolution characterization of their genotypic differences has been stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages. This analysis identified hamster genes missing in different CHO cell lines, and detected >3.7 million single-nucleotide polymorphisms (SNPs), 551,240 indels and 7,063 copy number variations. Many mutations are located in genes with functions relevant to bioprocessing, such as apoptosis. The details of this genetic diversity highlight the value of the hamster genome as the reference upon which CHO cells can be studied and engineered for protein production.

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“…Nevertheless, changes in sequencing and mapping technologies are gradually making this process easier and more rapid (Chin et al, 2013, Dong et al, 2013, and the Schistosoma genome is starting to be used to study anthelminthic resistance. For example, WGS facilitated the finding of the locus responsible for oxamniquine resistance in Schistosoma mansoni (Smp_089320) by providing an easy means to generate SNPs between parental lines in a staged genetic cross (Valentim et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Modelling the Effects of Mass Drug Administration on the Molecular Epidemiology of Schistosomes

Lamberton¹,

Crellen²,

Cotton³

et al. 2015

Mathematical Models for Neglected Tropical Diseases: Essential Tools for Control and Elimination, Part A

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Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Cited by 447 publications

References 63 publications

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

Modelling the Effects of Mass Drug Administration on the Molecular Epidemiology of Schistosomes

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