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Evolutionary Constraint in Flanking Regions of Avian Genes
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.
2011 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 28, no 9, 2481-2489 p.Article in journal (Refereed) Published
Abstract [en]

An important comprehension from comparative genomic analysis is that sequence conservation beyond neutral expectations is frequently found outside protein-coding regions, indicating important functional roles of noncoding DNA. Understanding the causes of constraint on noncoding sequence evolution forms an important area of research, not least in light of the importance for understanding the evolution of gene expression. We aligned all orthologous genes of chicken and zebra finch together with 5 kb of their upstream and downstream noncoding sequences, to study the evolution of gene flanking sequences in the avian genome. Using ancestral repeats as a neutral reference, we detected significant evolutionary constraint in the 3' flanking region, highest directly after termination (60%) and then gradually decreasing to about 20% 5 kb downstream. Constraint was higher in annotated 3' untranslated regions (UTRs) than in non-UTRs at the same distance from the stop codon and higher in sequences annotated as microRNA (miRNA)-binding sites than in non-miRNA-binding sites within 3' UTRs. Constraint was also higher when estimated for a smaller data set of genes from more closely related songbird species, indicating turnover of functional elements during avian evolution. On the 5' flanking side constraint was readily seen within the first 125 bp immediately upstream of the start codon (34%) and was about 10% for remaining sequence within 5 kb upstream. Analysis of chicken polymorphism data gave further support for the highest constraint directly before and after the translated region. Finally, we found that genes evolving under the highest constraint measured by d(N)/d(S) also had the highest level of constraint in the 3' flanking region. This study broadens the insights into gene flanking sequence evolution by adding new findings from a vertebrate lineage other than mammals.

Place, publisher, year, edition, pages
2011. Vol. 28, no 9, 2481-2489 p.
Keyword [en]
UTR, non-coding DNA, purifying selection, chicken, zebra finch
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-158881DOI: 10.1093/molbev/msr066ISI: 000294552700010OAI: oai:DiVA.org:uu-158881DiVA: diva2:442024
Available from: 2011-09-20 Created: 2011-09-19 Last updated: 2011-12-01Bibliographically approved
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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