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Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J - Open Biol (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden. biao.wang@ebc.uu.se

ABSTRACT
The black grouse (Tetrao tetrix) is a galliform bird species that is important for both 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.

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Distribution of the immune-related GO terms. The transcripts with immune functions were assigned to all levels of immune-related GO terms. The top 17 of the represented terms are shown and the rest are binned at the bottom.
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RSOB120054F3: Distribution of the immune-related GO terms. The transcripts with immune functions were assigned to all levels of immune-related GO terms. The top 17 of the represented terms are shown and the rest are binned at the bottom.

Mentions: To further focus on the identification of genes with immune function, we extracted 257 GO terms, including the GO level 2 term ‘immune system process’ and all its children terms, for chicken. On the basis of these GO annotations, we extracted 523 chicken immune-related gene sequences from Ensembl. Another stand-alone BLAST search was performed with our transcripts against these immune-related chicken genes, where we found 564 black grouse transcripts that matched to 308 homologous immune genes in the chicken. These black grouse transcripts had a mean length of 449 ± 236 bp. Our black grouse transcript set, although relatively modest in size, appears to contain homologues to a majority (58.9%) of all the extracted chicken immune genes. This percentage is notably higher than the percentage of all Ensembl chicken genes with matches in the grouse spleen in this study (38.2%). We expect that this is probably due to the highly enriched immune function of the spleen tissue we sequenced. The annotated immune genes are involved in a diversity of immune functions, including lymphocyte activation, T-cell activation, B-cell activation and various immune regulations (figure 3).Figure 3.


Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J - Open Biol (2012)

Distribution of the immune-related GO terms. The transcripts with immune functions were assigned to all levels of immune-related GO terms. The top 17 of the represented terms are shown and the rest are binned at the bottom.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376728&req=5

RSOB120054F3: Distribution of the immune-related GO terms. The transcripts with immune functions were assigned to all levels of immune-related GO terms. The top 17 of the represented terms are shown and the rest are binned at the bottom.
Mentions: To further focus on the identification of genes with immune function, we extracted 257 GO terms, including the GO level 2 term ‘immune system process’ and all its children terms, for chicken. On the basis of these GO annotations, we extracted 523 chicken immune-related gene sequences from Ensembl. Another stand-alone BLAST search was performed with our transcripts against these immune-related chicken genes, where we found 564 black grouse transcripts that matched to 308 homologous immune genes in the chicken. These black grouse transcripts had a mean length of 449 ± 236 bp. Our black grouse transcript set, although relatively modest in size, appears to contain homologues to a majority (58.9%) of all the extracted chicken immune genes. This percentage is notably higher than the percentage of all Ensembl chicken genes with matches in the grouse spleen in this study (38.2%). We expect that this is probably due to the highly enriched immune function of the spleen tissue we sequenced. The annotated immune genes are involved in a diversity of immune functions, including lymphocyte activation, T-cell activation, B-cell activation and various immune regulations (figure 3).Figure 3.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 75236 Uppsala, Sweden. biao.wang@ebc.uu.se

ABSTRACT
The black grouse (Tetrao tetrix) is a galliform bird species that is important for both 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.

Show MeSH