In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae).

Autor: Choi IS; Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA. Electronic address: 86ischoi@gmail.com., Wojciechowski MF; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA. Electronic address: mfwojciechowski@asu.edu., Ruhlman TA; Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: truhlman@austin.utexas.edu., Jansen RK; Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: jansen@austin.utexas.edu.
Jazyk: angličtina
Zdroj: Molecular phylogenetics and evolution [Mol Phylogenet Evol] 2021 Oct; Vol. 163, pp. 107236. Date of Electronic Publication: 2021 Jun 18.
DOI: 10.1016/j.ympev.2021.107236
Abstrakt: Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
(Copyright © 2021 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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