Abstract
BackgroundThe different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. The advent of the next generation sequencing technologies has made it possible to study which genomic regions are evolutionary liable to change and which are static, as well as enabling an increasing number of genome studies of non-model species. However, de novo sequencing of the whole genome of an organism remains non-trivial. In this study, we present the draft genome of the black grouse, which was developed using a reference-guided assembly strategy.ResultsWe generated 133 Gbp of sequence data from one black grouse individual by the SOLiD platform and used a combination of de novo assembly and chicken reference genome mapping to assemble the reads into 4572 scaffolds with a total length of 1022 Mb. The draft genome well covers the main chicken chromosomes 1 ~ 28 and Z which have a total length of 1001 Mb. The draft genome is fragmented, but has a good coverage of the homologous chicken genes. Especially, 33.0% of the coding regions of the homologous genes have more than 90% proportion of their sequences covered. In addition, we identified ~1 M SNPs from the genome and identified 106 genomic regions which had a high nucleotide divergence between black grouse and chicken or between black grouse and turkey.ConclusionsOur results support the hypothesis that the chromosome X (Z) evolves faster than the autosomes and our data are consistent with the MHC regions being more liable to change than the genome average. Our study demonstrates how a moderate sequencing effort can be combined with existing genome references to generate a draft genome for a non-model species.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-180) contains supplementary material, which is available to authorized users.
Highlights
The different regions of a genome do not evolve at the same rate
SOLiD sequencing The raw sequencing data was comprised of 793 M reads with a read length of 75 bp which were generated for the single-end library, 1642 M reads with read length of 60 bp × 60 bp which were generated for the 2 Kb matepaired library, and 1548 M reads with read length of 60 bp × 60 bp which were generated for the 5 Kb matepaired library
The continuously sequenced blocks on the scaffolds are fragmented, the draft genome has a good coverage of the homologous chicken genes, and 14826 (82.7%) of the chicken genes were identified on the black grouse draft genome
Summary
The different regions of a genome do not evolve at the same rate. For example, comparative genomic studies have suggested that the sex chromosomes and the regions harbouring the immune defence genes in the Major Histocompatability Complex (MHC) may evolve faster than other genomic regions. Generation sequencing (NGS) has spurred a revolution in the development of genomic tools for non-model organisms [1]. Sequencing complete transcriptomes [2] or complexity-reduced fractions of genomes [3] has enabled the identification of genome-wide molecular markers such as single nucleotide polymorphisms (SNPs) and microsatellites (SSRs). Such investigations have addressed fundamental questions in molecular ecology and evolution, such as the genomic basis for speciation [4,5],.
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