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De-novo emergence of SINE retroposons during the early evolution of passerine birds
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. University of Münster, Institute of Experimental Pathology (ZMBE).ORCID iD: 0000-0002-8979-9992
University of Münster, Institute of Experimental Pathology (ZMBE).
South Australian Museum, Adelaide; The University of Adelaide, School of Biological Sciences.
National Research Collections Australia, CSIRO, Australian National Wildlife Collection.
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2017 (English)In: Mobile DNA, ISSN 1759-8753, E-ISSN 1759-8753, Vol. 8, article id 21Article in journal (Refereed) Published
Abstract [en]

Background: Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes.

Results: Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching.

Conclusions: We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

Place, publisher, year, edition, pages
2017. Vol. 8, article id 21
Keywords [en]
Transposon, Retroposon, SINE, Birds, Passeriformes, Phylogenomics
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-339789DOI: 10.1186/s13100-017-0104-1ISI: 000417951700001PubMedID: 29255493OAI: oai:DiVA.org:uu-339789DiVA, id: diva2:1183443
Funder
German Research Foundation (DFG), KR3639Available from: 2018-02-16 Created: 2018-02-16 Last updated: 2018-02-16Bibliographically approved

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