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LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes
KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-0738-1574
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2017 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 12, p. 3449-3462Article in journal (Refereed) Published
Abstract [en]

The accumulat on and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.

Place, publisher, year, edition, pages
Oxford University Press, 2017. Vol. 9, no 12, p. 3449-3462
Keywords [en]
gymnosperm, Picea, Pinus, angiosperm, retroelement, gene conversion, recombination suppression, genome size
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:kth:diva-223298DOI: 10.1093/gbe/evx260ISI: 000423460600017PubMedID: 29228262Scopus ID: 2-s2.0-85042161256OAI: oai:DiVA.org:kth-223298DiVA, id: diva2:1183261
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180216

Available from: 2018-02-16 Created: 2018-02-16 Last updated: 2018-02-16Bibliographically approved

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Giacomello, Stefania

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