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dc.contributor.authorWang, Biao
dc.contributor.authorEkblom, Robert
dc.contributor.authorBunikis, Ignas
dc.contributor.authorSiitari, Heli
dc.contributor.authorHöglund, Jacob
dc.date.accessioned2014-08-13T10:26:57Z
dc.date.available2014-08-13T10:26:57Z
dc.date.issued2014
dc.identifier.citationWang, 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. <i>BMC Genomics</i>, <i>15</i>(180). <a href="https://doi.org/10.1186/1471-2164-15-180" target="_blank">https://doi.org/10.1186/1471-2164-15-180</a>
dc.identifier.otherCONVID_23676654
dc.identifier.otherTUTKAID_61864
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/44009
dc.description.abstractBackground: 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.fi
dc.language.isoeng
dc.publisherBioMed Central Ltd.
dc.relation.ispartofseriesBMC Genomics
dc.relation.urihttp://www.biomedcentral.com/1471-2164/15/180
dc.subject.otherTetrao tetrix
dc.titleWhole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-201408132350
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.contributor.oppiaineEkologia ja evoluutiobiologiafi
dc.contributor.oppiaineEcology and Evolutionary Biologyen
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.date.updated2014-08-13T03:32:43Z
dc.type.coarjournal article
dc.description.reviewstatuspeerReviewed
dc.relation.issn1471-2164
dc.relation.numberinseries180
dc.relation.volume15
dc.type.versionpublishedVersion
dc.rights.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.
dc.rights.accesslevelopenAccessfi
dc.subject.ysoteeri
jyx.subject.urihttp://www.yso.fi/onto/yso/p10259
dc.rights.urlhttp://creativecommons.org/licenses/by/2.0
dc.relation.doi10.1186/1471-2164-15-180


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© 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.
Except where otherwise noted, this item's license is described as © 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.