Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
1 Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
2 Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, SE-75237, Uppsala, Sweden
3 Department of Biological and Environmental Science, University of Jyväskylä, P. O. Box 35, FI-40014 Jyväskylä, Finland
BMC Genomics 2014, 15:180 doi:10.1186/1471-2164-15-180Published: 6 March 2014
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. 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.
We 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.
Our 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.