Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome 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. 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-trnW-CCA) 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. 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.

中文翻译：

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Avena的比较叶绿体基因组分析：进化动力学和系统发育的见解。

燕麦（Avena sativa L.）是公认的保健食品，其不同的候选A基因组祖先物种的贡献尚无定论。在这里，我们报告11种燕麦属植物的叶绿体基因组序列，以检查质体进化动力学，并分析燕麦及其同类野生相关物种之间的系统发育关系。11种Avena物种的叶绿体基因组（大小范围为135,889–135,998 bp）共有四方结构，包括一个大的单拷贝（LSC； 80,014–80,132 bp），一个小的单拷贝（SSC； 12,575–12,679 bp）和一对反向重复序列（IR； 21,603–21,614 bp）。质体组包含131个基因，其中包括84个蛋白质编码基因，8个核糖体RNA和39个转移RNA。核苷酸序列多样性（Pi值）的范围是0.0036（rps19）至0。十个最多态的基因为0093（rpl32），十个最多态的基因间区域为0.0084（psbH-petB）至0.0240（petG-trnW-CCA）。基因选择性压力分析表明，所有蛋白质编码基因均已处于纯化选择之下。串联重复序列，插入/缺失和单核苷酸多态性之间的相邻位置关系支持了串联重复序列在引起Avena质体突变方面的进化重要性。基于完整的质体组序列和LSC分子间重组序列的系统生物学分析支持属属中有两个进化枝的Avena单性系。Avena质体组的多样性是由高度多样化的基因和基因间区域，LSC分子间重组，并同时出现串联重复和插入缺失或单核苷酸多态性。研究表明，A基因组二倍体-多倍体谱系维持着两个不同母系祖先的亚进化枝，长枝曲霉是进化枝I中的第一个分化物种。在燕麦属和禾本科科水平上的动态变化，对于利用质体组变异来制备用于植物育种的杂种可能很有用。