Comparative chloroplast genome analyses of Avena : insights into evolutionary dynamics and phylogeny
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RESEARCH ARTICLE
Open Access
Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny Qing Liu1,2* , Xiaoyu Li1,3, Mingzhi Li4, Wenkui Xu4, Trude Schwarzacher1,5 and John Seymour Heslop-Harrison1,5*
Abstract Background: Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate Agenome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species. Results: The chloroplast genomes of eleven Avena species (size range of 135,889–135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014–80,132 bp), a small single copy (SSC; 12,575–12,679 bp) and a pair of inverted repeats (IRs; 21,603–21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnWCCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/ deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus. Conclusions: Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding. Keywords: Avena, Chloroplast genome, Evolution rate, Insertions/deletions, Intermolecular recombination, Phylogenomics, Single nucleotide polymorphisms, Tandem repeats
* Correspondence: [email protected]; [email protected] 1 Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which pe
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