| 1. |
- Warren, Wesley C, et al.
(author)
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The genome of a songbird
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 757-762
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Journal article (peer-reviewed)abstract
- The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
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| 2. |
- Balakrishnan, Christopher N., et al.
(author)
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Gene duplication and fragmentation in the zebra finch major histocompatibility complex
- 2010
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In: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 8, s. 29-
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Journal article (peer-reviewed)abstract
- Background: Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. Results: The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. Conclusion: The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.
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| 3. |
- Dawson, Deborah, et al.
(author)
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High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species
- 2013
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14:1, s. 176-
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Journal article (peer-reviewed)abstract
- Background: Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotypinga wide range of species would not only save resources but also uniquely enablenew comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avianmicrosatellite markers with enhanced cross-species utility. Results: We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utilityby genotyping individuals belonging to eight passerine and four non-passerinespecies. The majority of the new Conserved Avian Microsatellite (CAM) markersamplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with amean 68% of loci polymorphic per species, compared with 42% in non-passerinespecies. Conclusions: When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense ofmicrosatellite isolation for a wide range of genetic studies, including avianparentage and population analyses, but will also now enable comparisons ofgenetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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| 4. |
- Ekblom, Robert, et al.
(author)
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A field guide to whole-genome sequencing, assembly and annotation
- 2014
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In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 7:9, s. 1026-1042
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Journal article (peer-reviewed)abstract
- Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
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| 5. |
- Ekblom, Robert, et al.
(author)
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Applications of next generation sequencing in molecular ecology of non-model organisms
- 2011
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In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 107:1, s. 1-15
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Research review (peer-reviewed)abstract
- As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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| 6. |
- Ekblom, Robert, et al.
(author)
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Balancing selection, sexual selection and geographic structure in MHC genes of Great Snipe
- 2010
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In: Genetica. - : Springer Science and Business Media LLC. - 0016-6707 .- 1573-6857. ; 138:4, s. 453-461
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Journal article (peer-reviewed)abstract
- Signatures of balancing selection are often found when investigating the extremely polymorphic regions of major histocompatibility complex (MHC) genes, and it is generally accepted that selective forces maintain this polymorphism. However, the exact nature of the selection is controversial. Theoretical studies have mainly focused on overdominance and/or frequency dependent selection while laboratory studies have emphasised the role of mate choice. Empirical field data, on the other hand, have been relatively scarce. Previously we have found that geographic structure in MHC class II genes of the Great Snipe (Gallinago media) is too pronounced to be explained by neutral forces alone. Here we test the hypothesis that sexual selection on MHC alleles may be influencing this geographic structure between mountain and lowland populations. We found evidence of balancing selection acting on MHC genes in the form of a higher rate of amino-acid changing substitutions compared to silent substitutions in the peptide binding regions. Not only natural selection but also sexual selection may influence MHC polymorphism in this bird because certain MHC alleles have been found to be associated with higher male mating success. Contrary to predictions from negative frequency dependent selection, males carrying locally rare alleles did not have a mating advantage. Instead, the mating success of alleles in a mountain population was positively correlated to their relative frequency in the mountains compared to the lowlands, implying that locally adapted MHC alleles may also be favoured by sexual selection.
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| 7. |
- Ekblom, Robert, et al.
(author)
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Characterization of the house sparrow (Passer domesticus) transcriptome : a resource for molecular ecology and immunogenetics
- 2014
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 14:3, s. 636-646
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Journal article (peer-reviewed)abstract
- The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.
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| 8. |
- Ekblom, Robert, et al.
(author)
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Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies
- 2012
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In: Comparative and functional genomics. - : Hindawi Limited. - 1531-6912 .- 1532-6268. ; 2012, s. 281693-
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Journal article (peer-reviewed)abstract
- Next-generation sequencing of transcriptomes (RNA-Seq) is being used increasingly in studies of nonmodel organisms. Here, we evaluate the effectiveness of normalising cDNA libraries prior to sequencing in a small-scale study of the zebra finch. We find that assemblies produced from normalised libraries had a larger number of contigs but used fewer reads compared to unnormalised libraries. Considerably more genes were also detected using the contigs produced from normalised cDNA, and microsatellite discovery was up to 73% more efficient in these. There was a positive correlation between the detected expression level of genes in normalised and unnormalised cDNA, and there was no difference in the number of genes identified as being differentially expressed between blood and spleen for the normalised and unnormalised libraries. We conclude that normalised cDNA libraries are preferable for many applications of RNA-Seq and that these can also be used in quantitative gene expression studies.
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| 9. |
- Ekblom, Robert, et al.
(author)
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Digital gene expression analysis of the zebra finch genome
- 2010
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11, s. 219-
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Journal article (peer-reviewed)abstract
- Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates.
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| 10. |
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| 11. |
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| 12. |
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Ekblom, Robert
(author)
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Evaluation of the analysis of distance sampling data : a simulation study
- 2010
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In: Ornis Svecica. - 1102-6812 .- 2003-2633. ; 20, s. 43-53
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Journal article (peer-reviewed)abstract
- Distance sampling is used to estimate number of indi- viduals in an area of interest. The idea is that with known distances to the observed individuals, one can model the probability of detection in relation to distance and thereby account for individuals that were not detected. Distances can be recorded either exactly or in discrete categories. In this study I validated the method using simulated dis- tance sampling data for two hypothetical bird species and compared the estimated density values to the known true densities. Generally the true densities and numbers of individuals were very similar to (and always within the 95% confidence interval of) the parameter estimates from the analysis of the simulated data. The analyses were also robust to modifications of the data such as truncation andgrouping of the distances into discrete categories. The confidence intervals increased, however, when using only two distance groups. Given that critical assumptions of the model can be met in the field situation, distance data can thus be used in a wide range of bird studies to calculate reliable density estimates.
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| 17. |
- Ekblom, Robert, et al.
(author)
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Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes
- 2010
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 2, s. 781-790
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Journal article (peer-reviewed)abstract
- Genes of the immune system are generally considered to evolve rapidly due to host-parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated d(N)/d(S) ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher d(N)/d(S) ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds.
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| 18. |
- Ekblom, Robert, et al.
(author)
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Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff
- 2012
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 2:10, s. 2485-2500
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Journal article (peer-reviewed)abstract
- By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black-and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation.
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| 19. |
- Ekblom, Robert, et al.
(author)
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Genetic mapping of the major histocompatibility complex in the zebra finch (Taeniopygia guttata)
- 2011
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In: Immunogenetics. - : Springer Science and Business Media LLC. - 0093-7711 .- 1432-1211. ; 63:8, s. 523-530
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Journal article (peer-reviewed)abstract
- Genes of the major histocompatibility complex (MHC) have received much attention in immunology, genetics, and ecology because they are highly polymorphic and play important roles in parasite resistance and mate choice. Until recently, the MHC of passerine birds was not well-described. However, the genome sequencing of the zebra finch (Taeniopygia guttata) has partially redressed this gap in our knowledge of avian MHC genes. Here, we contribute further to the understanding of the zebra finch MHC organization by mapping SNPs within or close to known MHC genes in the zebra finch genome. MHC class I and IIB genes were both mapped to zebra finch chromosome 16, and there was no evidence that MHC class I genes are located on chromosome 22 (as suggested by the genome assembly). We confirm the location in the MHC region on chromosome 16 for several other genes (BRD2, FLOT1, TRIM7.2, GNB2L1, and CSNK2B). Two of these (CSNK2B and FLOT1) have not previously been mapped in any other bird species. In line with previous results, we also find that orthologs to the immune-related genes B-NK and CLEC2D, which are part of the MHC region in chicken, are situated on zebra finch chromosome Z and not among other MHC genes in the zebra finch.
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| 20. |
- Ekblom, Robert, et al.
(author)
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Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 467-
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Journal article (peer-reviewed)abstract
- Background: Genome and transcriptome sequencing applications that rely on variation in sequence depth can be negatively affected if there are systematic biases in coverage. We have investigated patterns of local variation in sequencing coverage by utilising ultra-deep sequencing (>100,000X) of mtDNA obtained during sequencing of two vertebrate genomes, wolverine (Gulo gulo) and collared flycatcher (Ficedula albicollis). With such extreme depth, stochastic variation in coverage should be negligible, which allows us to provide a very detailed, fine-scale picture of sequence dependent coverage variation and sequencing error rates. Results: Sequencing coverage showed up to six-fold variation across the complete mtDNA and this variation was highly repeatable in sequencing of multiple individuals of the same species. Moreover, coverage in orthologous regions was correlated between the two species and was negatively correlated with GC content. We also found a negative correlation between the site-specific sequencing error rate and coverage, with certain sequence motifs "CCNGCC" being particularly prone to high rates of error and low coverage. Conclusions: Our results demonstrate that inherent sequence characteristics govern variation in coverage and suggest that some of this variation, like GC content, should be controlled for in, for example, RNA-Seq and detection of copy number variation.
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| 21. |
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| 23. |
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| 26. |
- Hellgren, Olof, et al.
(author)
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Evolution of a cluster of innate immune genes (beta-defensins) along the ancestral lines of chicken and zebra finch
- 2010
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In: Immunome Research. - : Springer Science and Business Media LLC. - 1745-7580. ; 6:3
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Journal article (peer-reviewed)abstract
- BACKGROUND: Avian beta-defensins (AvBDs) represent a group of innate immune genes with broad antimicrobial activity. Within the chicken genome, previous work identified 14 AvBDs in a cluster on chromosome three. The release of a second bird genome, the zebra finch, allows us to study the comparative evolutionary history of these gene clusters between from two species that shared a common ancestor about 100 million years ago.RESULTS: A phylogenetic analysis of the beta-defensin gene clusters in the chicken and the zebra finch identified several cases of gene duplication and gene loss along their ancestral lines. In the zebra finch genome a cluster of 22 AvBD genes were identified, all located within 125 Kbp on chromosome three. Ten of the 22 genes were found to be highly conserved with orthologous genes in the chicken genome. The remaining 12 genes were all located within a cluster of 58 Kbp and are suggested to be a result of recent gene duplication events that occurred after the galliformes- passeriformes split (G-P split). Within the chicken genome, AvBD6 was found to be a duplication of AvBD7, whereas the gene AvDB14 seems to have been lost along the ancestral line of the zebra finch. The duplicated beta-defensin genes have had a significantly higher accumulation of non-synonymous over synonymous substitutions compared to the genes that have not undergone duplication since the G-P split. The expression patterns of avian beta-defensin genes seem to be well conserved between chicken and zebra finch.CONCLUSION: The genomic comparisons of the beta-defensins gene clusters of the chicken and zebra finch illuminate the evolutionary history of this gene complex. Along their ancestral lines, several gene duplication events have occurred in the passerine line after the galliformes-passeriformes split giving rise to 12 novel genes compared to a single duplication event in the galliformes line. After the duplication events, the duplicated genes have been subject to a relaxed selection pressure compared to the non-duplicated genes, thus supporting models of evolution by gene duplication.
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| 27. |
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| 28. |
- Stapley, Jessica, et al.
(author)
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Adaptation genomics : the next generation
- 2010
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In: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 25:12, s. 705-712
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Research review (peer-reviewed)abstract
- Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that( have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic: variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?
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| 29. |
- Wang, Biao, et al.
(author)
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Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC
- 2012
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 13, s. 553-
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Journal article (peer-reviewed)abstract
- Background: The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicken MHC-B genomic region has a highly streamlined gene content compared to mammalian MHCs. Its core region includes genes encoding Class I and Class IIB molecules but is only similar to 92Kb in length. Sequences of other galliform MHCs show varying degrees of similarity as that of chicken. The black grouse (Tetrao tetrix) is a wild galliform bird species which is an important model in conservation genetics and ecology. We sequenced the black grouse core MHC-B region and combined this with available data from related species (chicken, turkey, gold pheasant and quail) to perform a comparative genomics study of the galliform MHC. This kind of analysis has previously been severely hampered by the lack of genomic information on avian MHC regions, and the galliformes is still the only bird lineage where such a comparison is possible. Results: In this study, we present the complete genomic sequence of the MHC-B locus of black grouse, which is 88,390 bp long and contains 19 genes. It shows the same simplicity as, and almost perfect synteny with, the corresponding genomic region of chicken. We also use 454-transcriptome sequencing to verify expression in 17 of the black grouse MHC-B genes. Multiple sequence inversions of the TAPBP gene and TAP1-TAP2 gene block identify the recombination breakpoints near the BF and BLB genes. Some of the genes in the galliform MHC-B region also seem to have been affected by selective forces, as inferred from deviating phylogenetic signals and elevated rates of non-synonymous nucleotide substitutions. Conclusions: We conclude that there is large synteny between the MHC-B region of the black grouse and that of other galliform birds, but that some duplications and rearrangements have occurred within this lineage. The MHC-B sequence reported here will provide a valuable resource for future studies on the evolution of the avian MHC genes and on links between immunogenetics and ecology of black grouse.
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| 30. |
- Wang, Biao, et al.
(author)
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Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
- 2012
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In: Open Biology. - : The Royal Society. - 2046-2441. ; 2, s. 120054-
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Journal article (peer-reviewed)abstract
- 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.
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| 31. |
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