Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Nature Biotechnology Year : 2013

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

Nianqing Xiao
  • Function : Author
Xin Liu
Bertrand Servin
Bin Zhu
  • Function : Author
Deacon Sweeney
  • Function : Author
Rich Moore
  • Function : Author
Thomas Faraut
James Kijas
  • Function : Author

Abstract

We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.

Dates and versions

hal-02651460 , version 1 (29-05-2020)

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Cite

Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, et al.. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 2013, 31 (2), pp.135-141. ⟨10.1038/nbt.2478⟩. ⟨hal-02651460⟩
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