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Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

Abstract
Background: 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. Results: 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. Conclusions: 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.
Main Authors
Format
Articles Research article
Published
2014
Series
Subjects
Publication in research information system
Publisher
BioMed Central Ltd.
Original source
http://www.biomedcentral.com/1471-2164/15/180
The permanent address of the publication
https://urn.fi/URN:NBN:fi:jyu-201408132350Use this for linking
Review status
Peer reviewed
ISSN
1471-2164
DOI
https://doi.org/10.1186/1471-2164-15-180
Language
English
Published in
BMC Genomics
Citation
  • Wang, B., Ekblom, R., Bunikis, I., Siitari, H., & Höglund, J. (2014). Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics, 15(180). https://doi.org/10.1186/1471-2164-15-180
License
CC BY 2.0Open Access
Copyright© 2014 Wang et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

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