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Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
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2012 (English)In: Open Biology, ISSN 2046-2441, E-ISSN 2046-2441, Vol. 2, 120054- p.Article in journal (Refereed) Published
Abstract [en]

The black grouse (Tetrao tetrix) is a galliform bird species that is important forboth ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species.

Place, publisher, year, edition, pages
2012. Vol. 2, 120054- p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-183642DOI: 10.1098/rsob.120054ISI: 000307112200005OAI: oai:DiVA.org:uu-183642DiVA: diva2:563639
Available from: 2012-10-31 Created: 2012-10-31 Last updated: 2017-12-07Bibliographically approved
In thesis
1. Development and Application of Genomic Resources in Non-model Bird Species
Open this publication in new window or tab >>Development and Application of Genomic Resources in Non-model Bird Species
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the genetic basis of biological processes is a fundamental component of modern ecology and evolutionary biology studies. With the recent advent of next generation sequencing (NGS) technologies, it is now possible to perform large genome and transcriptome projects for ecologically important non-model species. In this thesis, I focused on the development and application of genomic resources of two non-model bird species, the black grouse (Tetrao tetrix) and the great snipe (Gallinago media). Using the chicken genome as a reference, I developed a reference guided NGS pipeline to assemble the complete draft genome of black grouse. The draft genome has a good coverage of the main 29 chromosomes of the chicken genome. The genome was used to develop a vast number of genetic markers. Comparing this genome with that of other species, I identified the genomic regions which were important for the lineage specific evolution of black grouse. I also sequenced and characterised the spleen transcriptome of the black grouse. I identified and validated a large number of gene-based microsatellite markers from the transcriptome and identified and confirmed the expression of immune related genes. Using a similar RNA-Seq approach, I also sequenced the blood transcriptomes of 14 great snipe males with different mating success. I identified genes and single nucleotide polymorphisms (SNPs) which might be related to male mating success in this species, both in terms of gene expression levels and genetic variation structure. For the immunologically important major histocompatibility complex (MHC) gene region of black grouse, I constructed a fosmid library and used it to sequence the complete core MHC region of this species. This resource allowed me to perform a comprehensive comparative genomics analysis of the galliform MHC, by which I found that some genes in this region were affected by selective forces. I was also able to develop a single locus genotyping protocol for the duplicated MHC BLB (class IIB) genes and found that the two black grouse BLB loci followed different evolutionary trajectories. This thesis set an example of developing genomic resources in non-model species and applying them in addressing questions relevant to ecology and evolutionary biology.

Place, publisher, year, edition, pages
Uppsala: Uppsala universitet, 2012. 49 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 999
Keyword
genome, transcriptome, next generation sequencing, non-model species, bioinformatics, reference guided assembly, RNA-Seq, comparative genomics, gene expression, major histocompatibility complex, single nucleotide polymorphism, microsatellite
National Category
Biological Sciences
Research subject
Biology
Identifiers
urn:nbn:se:uu:diva-183645 (URN)978-91-554-8540-5 (ISBN)
Public defence
2012-12-14, Lindahlssalen, Norbyvägen 18B, Uppsala, 14:00 (English)
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Supervisors
Available from: 2012-11-26 Created: 2012-10-31 Last updated: 2013-07-22

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