Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Dalrymple, Brian P.; Kirkness, Ewen F.; Nefedov, Mikhail; McWilliam, Sean; Ratnakumar, Abhirami; Barris, Wes; Zhao, Shaying; Shetty, Jyoti; Maddox, J F; O'Grady, Margaret; Nicholas, F. W.; Crawford, A. M.; Smith, Ted; Jong, Pieter J. de; McEwan, John C.; Oddy, V. H.; Cockett, Noelle E.

doi:10.1186/gb-2007-8-7-r152

Cited by 80 publications

(85 citation statements)

References 40 publications

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“…The different stages of the reference genome assemblies of the two species may also have played a role. The sheep genome has been the subject of several improvements and refinements (Maddox et al, 2001;Goldammer et al, 2009), including the development of a virtual genome map based on bovine, dog and human genome assemblies (Dalrymple et al, 2007). These efforts culminated in the first draft of the ovine reference genome (Archibald et al, 2010), which has been improved further and the current released reference assembly, Oar v3.1, has a contig N50 length of~40 Kb and a total assembled length of 2.61 Gb, with~99% anchored onto the 26 autosomes and the X chromosome (Jiang et al, 2014).…”

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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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%

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

et al. 2015

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“…These applications make RNA-Seq technology a powerful tool for in-depth research on complex transcriptomes. The International Sheep Genome Consortium utilizes the results from the Human Genome Project; moreover, genomic research for the dog and cow is used to derive a virtual sheep genome map (Dalrymple et al, 2007;Archibald et al, 2010). However, these are currently available only for low-coverage genome sequences (Archibald et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

Yuan¹,

Liu²,

Yang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Wool is produced via synthetic processes of wool follicles, which are embedded in the skin of sheep. The development of new-generation sequencing and RNA sequencing provides new approaches that may elucidate the molecular regulation mechanism of wool follicle development and facilitate enhanced selection for wool traits through gene-assisted selection or targeted gene manipulation. We performed de novo transcriptome sequencing of skin using the Illumina Hiseq 2000 sequencing system in sheep (Ovis aries). Transcriptome de novo assembly was carried out via short-read assembly programs, including SOAPdenovo and ESTScan. The protein function, clusters of orthologous group function, gene ontology function, metabolic pathway analysis, and protein coding region prediction of unigenes were annotated by BLASTx, BLAST2GO, and ESTScan. More than 26,266,670 clean reads were collected and assembled into 79,741 unigene sequences, with a final assembly length of 35,447,962 nucleotides. A total of 22,164 unigenes were annotated, accounting for Y.J. Yue et al. 1372©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (1): 1371-1384 (2015) 36.27% of the total number of unigenes, which were divided into 25 classes belonging to 218 signaling pathways. Among them, there were 17 signal paths related to hair follicle development. Based on mass sequencing data of sheepskin obtained by RNA-Seq, many unigenes were identified and annotated, which provides an excellent platform for future sheep genetic and functional genomic research. The data could be used for improving wool quality and as a model for human hair follicle development or disease prevention.

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“…Organisms lacking complete genome assembly and annotation may rely on comparative alignments to wellannotated species to relate markers to genomic features (Dalrymple et al, 2007). As of this writing, the Bos taurus (Bovine Genome Sequencing and Analysis Consortium, 2009;Zimin et al, 2009) and horse (Wade et al, 2009) genome assemblies and annotation may be the most mature of any livestock species.…”

Section: Genome Annotation and Functional Informationmentioning

confidence: 99%

BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection1–3

Snelling

Cushman

Keele

et al. 2013

Journal of Animal Science

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Many traits affecting profi tability and sustainability of meat, milk, and fi ber production are polygenic, with no single gene having an overwhelming infl uence on observed variation. No knowledge of the specifi c genes controlling these traits has been needed to make substantial improvement through selection. Signifi cant gains have been made through phenotypic selection enhanced by pedigree relationships and continually improving statistical methodology. Genomic selection, recently enabled by assays for dense SNP located throughout the genome, promises to increase selection accuracy and accelerate genetic improvement by emphasizing the SNP most strongly correlated to phenotype although the genes and sequence variants affecting phenotype remain largely unknown. These genomic predictions theoretically rely on linkage disequilibrium (LD) between genotyped SNP and unknown functional variants, but familial linkage may increase effectiveness when predicting individuals related to those in the training data. Genomic selection with functional SNP genotypes should be less reliant on LD patterns shared by training and target populations, possibly allowing robust prediction across unrelated populations.

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Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Cited by 80 publications

References 40 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

De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries)

BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection1–3

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