Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

作者：Suh Alexander; Smeds Linnea; Ellegren Hans

来源：Molecular Ecology, 2018, 27(1): 99-111.

DOI：10.1111/mec.14439

<jats:title>Abstract</jats:title><jats:p>Transposable elements (<jats:styled-content style="fixed-case">TE</jats:styled-content>s) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, <jats:styled-content style="fixed-case">DNA</jats:styled-content> methylation and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of <jats:styled-content style="fixed-case">TE</jats:styled-content>s in their genomes and this has been attributed to a potential dearth in transposition during their evolution. Here, we show that avian evolution witnessed diverse and abundant transposition on very recent timescales. First, we made an in‐depth repeat annotation of the collared flycatcher genome, including identification of 23 new, retrovirus‐like <jats:styled-content style="fixed-case">LTR</jats:styled-content> retrotransposon families. Then, using whole‐genome resequencing data from 200 <jats:italic>Ficedula</jats:italic> flycatchers, we detected 11,888 polymorphic <jats:styled-content style="fixed-case">TE</jats:styled-content> insertions (TE presence/absence variations, <jats:styled-content style="fixed-case">TEV</jats:styled-content>s) that segregated within and among species. The density of <jats:styled-content style="fixed-case">TEV</jats:styled-content>s was one every 1.5–2.5 Mb per individual, with heterozygosities of 0.12–0.16. The majority of <jats:styled-content style="fixed-case">TEV</jats:styled-content>s belonged to some 10 different <jats:styled-content style="fixed-case">LTR</jats:styled-content> families, most of which are specific to the flycatcher lineage. <jats:styled-content style="fixed-case">TEV</jats:styled-content>s were validated by tracing the segregation of hundreds of <jats:styled-content style="fixed-case">TEV</jats:styled-content>s across a three‐generation pedigree of collared flycatchers and also by their utility as markers recapitulating the phylogenetic relationships among flycatcher species. Our results suggest frequent germline invasions of songbird genomes by novel retroviruses as a rich source of structural variation, which may have had underappreciated phenotypic consequences for the diversification of this species‐rich group of birds.</jats:p>

• 出版日期2018-1