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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
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, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
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2010 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no Suppl.1, 266-276 p.Article in journal (Refereed) Published
Abstract [en]

Next-generation sequencing technology provides an attractive means to obtain largescale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with ∼1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with x as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.

Place, publisher, year, edition, pages
2010. Vol. 19, no Suppl.1, 266-276 p.
Keyword [en]
Avian genomics, Hill-Robertson effect, Male-mutation bias, Next generation sequencing 454, Selection
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-136234DOI: 10.1111/j.1365-294X.2009.04487.xISI: 000275645700021PubMedID: 20331785OAI: oai:DiVA.org:uu-136234DiVA: diva2:376501
Available from: 2010-12-10 Created: 2010-12-10 Last updated: 2016-04-26
In thesis
1. Birds as a Model for Comparative Genomic Studies
Open this publication in new window or tab >>Birds as a Model for Comparative Genomic Studies
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Comparative genomics provides a tool to investigate large biological datasets, i.e. genomic datasets. In my thesis I focused on inferring patterns of selection in coding and non-coding regions of avian genomes. Until recently, large comparative studies on selection were mainly restricted to model species with sequenced genomes. This limitation has been overcome with advances in sequencing technologies and it is now possible to gather large genomic data sets for non-model species. 

Next-generation sequencing data was used to study patterns of nucleotide substitutions and from this we inferred how selection has acted in the genomes of 10 non-model bird species. In general, we found evidence for a negative correlation between neutral substitution rate and chromosome size in birds. In a follow up study, we investigated two closely related bird species, to study expression levels in different tissues and pattern of selection. We found that between 2% and 18% of all genes were differentially expressed between the two species.

We showed that non-coding regions adjacent to genes are under evolutionary constraint in birds, which suggests that noncoding DNA plays an important functional role in the genome. Regions downstream to genes (3’) showed particularly high level of constraint. The level of constraint in these regions was not correlated to the length of untranslated regions, which suggests that other causes play also a role in sequence conservation.

We compared the rate of nonsynonymous substitutions to the rate of synonymous substitutions in order to infer levels of selection in protein-coding sequences. Synonymous substitutions are often assumed to evolve neutrally. We studied synonymous substitutions by estimating constraint on 4-fold degenerate sites of avian genes and found significant evolutionary constraint on this category of sites (between 24% and 43%). These results call for a reappraisal of synonymous substitution rates being used as neutral standards in molecular evolutionary analysis (e.g. the dN/dS ratio to infer positive selection).

Finally, the problem of sequencing errors in next-generation sequencing data was investigated. We developed a program that removes erroneous bases from the reads. We showed that low coverage sequencing projects and large genome sequencing projects will especially gain from trimming erroneous reads.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2011. 62 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 868
Birds, Selection, Gene expression, Sequence evolution, Next-generation sequencing, Comparative genomics, Molecular evolution, Genomics, Substitution Rates, Non-coding DNA
National Category
Evolutionary Biology Bioinformatics and Systems Biology
Research subject
Biology with specialization in Molecular Evolution
urn:nbn:se:uu:diva-159766 (URN)978-91-554-8186-5 (ISBN)
Public defence
2011-11-25, Lindahlsalen, Evolutionary Biology Centre, Norbyvägen 18A, Uppsala, 13:00 (English)
Available from: 2011-11-04 Created: 2011-10-10 Last updated: 2011-11-10Bibliographically approved

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