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Gene content and patterns of gene expression in the flycatcher genome
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Phenotypic evolution may be driven by changes in the sequence of protein-coding genes or by the way (when, where, at what level) proteins are expressed. Generally, our knowledge about the evolution of gene expression is relatively limited, and this is particularly so for wild populations. Collared flycatcher (Ficedula albicollis) and pied flycatcher (F. hypoleuca) are two recently diverged passerine birds, which have been subject to extensive ecological research, including aspects of speciation. We obtained RNA-seq data with Illumina technology from 10 adult individuals per species (five females and five males) using brain, kidney, liver, lung, muscle, skin, ovary, and testis tissue (plus eight embryos of each species). A total of more than 1 billion sequencing reads were assembled into >15.000 gene models for each species. The proportion of differentially expressed genes between species ranged from 8% to 18% per adult tissue. Very few GO categories were found to be overrepresented among differentially expressed genes, which at least in part might reflect that orphan and not yet annotated genes are prone to evolve more rapidly in gene expression level. However, in testis, the category olfactory receptor activity was significantly overrepresented among differentially expressed genes and it is of interest to note that this category of genes is involved in sperm-egg communication and thereby potentially may contribute to reproductive incompatibility between the two species. Genes with a high degree of differentiation in gene expression between species tended to have high rates of sequence evolution (high dN/dS). Overall, this study illustrates both the feasibility and usefulness of deep transcriptome sequencing in non-model organisms.

Keyword [en]
Collared flycatcher, Pied flycatcher, Zebra finch, RNA-Seq, Transcriptome sequencing, Species comparison, Gene expression
National Category
Evolutionary Biology
URN: urn:nbn:se:uu:diva-159916OAI: oai:DiVA.org:uu-159916DiVA: diva2:447422
Available from: 2011-10-11 Created: 2011-10-11 Last updated: 2011-11-10
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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