An Update of the Goat Genome Assembly Using Dense Radiation Hybrid Maps Allows Detailed Analysis of Evolutionary Rearrangements in Bovidae

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2014 Jul 24

PMID 25052253

Citations 10

Authors

Xiaoyong Du

Bertrand Servin

James E Womack

Jianhua Cao

Mei Yu

Yang Dong

Wen Wang

Shuhong Zhao

Affiliations

Soon will be listed here.

Abstract

Background: The domestic goat (Capra hircus), an important livestock species, belongs to a clade of Ruminantia, Bovidae, together with cattle, buffalo and sheep. The history of genome evolution and chromosomal rearrangements on a small scale in ruminants remain speculative. Recently completed goat genome sequence was released but is still in a draft stage. The draft sequence used a variety of assembly packages, as well as a radiation hybrid (RH) map of chromosome 1 as part of its validation.

Results: Using an improved RH mapping pipeline, whole-genome dense maps of 45,953 SNP markers were constructed with statistical confidence measures and the saturated maps provided a fine map resolution of approximate 65 kb. Linking RH maps to the goat sequences showed that the assemblies of scaffolds/super-scaffolds were globally accurate. However, we observed certain flaws linked to the process of anchoring chromosome using conserved synteny with cattle. Chromosome assignments, long-range order, and orientation of the scaffolds were reassessed in an updated genome sequence version. We also present new results exploiting the updated goat genome sequence to understand genomic rearrangements and chromosome evolution between mammals during species radiations. The sequence architecture of rearrangement sites between the goat and cattle genomes presented abundant segmental duplication on regions of goat chromosome 9 and 14, as well as new insertions in homologous cattle genome regions. This complex interplay between duplicated sequences and Robertsonian translocations highlights the rearrangement mechanism of centromeric nonallelic homologous recombination (NAHR) in mammals. We observed that species-specific shifts in ANKRD26 gene duplication are coincident with breakpoint reuse in divergent lineages and this gene family may play a role in chromosome stabilization in chromosome evolution.

Conclusions: We generated dense maps of the complete whole goat genome. The chromosomal maps allowed us to anchor and orientate assembled genome scaffolds along the chromosomes, annotate chromosome rearrangements and thereby get a better understanding of the genome evolution of ruminants and other mammals.

Citing Articles

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A near complete genome for goat genetic and genomic research.

Li R, Yang P, Dai X, Nanaei H, Fang W, Yang Z Genet Sel Evol. 2021; 53(1):74.

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The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat.

Xiao C, Li J, Xie T, Chen J, Zhang S, Elaksher S Ecol Evol. 2021; 11(12):7779-7795.

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Detection of myostatin gene MSTN in some goat breeds ().

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