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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燕麦叶绿体基因组的比较分析：对进化动力学和系统发育的见解。


燕麦 (Avena sativa L.) 是一种公认​​的健康食品，其不同候选 A 基因组祖先物种的贡献仍无定论。在这里，我们报告了十一个燕麦物种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属野生相关物种之间的系统发育关系。十一个燕麦物种的叶绿体基因组（大小范围为 135,889–135,998 bp）共享四部分结构，包括一个大单拷贝（LSC；80,014–80,132 bp）、一个小单拷贝（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。十个多态性最强的基因的核苷酸序列多样性（Pi值）范围为0.0036（rps19）至0.0093（rpl32），十个多态性最强的基因间区域的核苷酸序列多样性（Pi值）范围为0.0084（psbH-petB）至0.0240（petG-trnW-CCA）。基因选择压力分析表明所有蛋白质编码基因都经过纯化选择。串联重复、插入/缺失和单核苷酸多态性之间的相邻位置关系支持串联重复在引起燕麦质体突变中的进化重要性。基于完整质体序列和 LSC 分子间重组序列的系统基因组分析支持燕麦属中具有两个进化枝的单系性。燕麦质体的多样化可以通过高度多样化的基因和基因间区域、LSC 分子间重组以及串联重复和插入缺失或单核苷酸多态性的共现来解释。 该研究表明，A基因组二倍体-多倍体谱系维持着两个源自不同母系祖先的亚支，其中A. longiglumis是支系I中第一个分化的物种。这些基因组资源将有助于阐明叶绿体基因组结构，了解进化过程。燕麦属和禾本科水平的动态，并且可能有助于利用质体变异来制造植物育种杂交种。