Barrett Craig F
Department of Biology, West Virginia University, Morgantown, WV, USA.
PeerJ. 2020 Jun 16;8:e9315. doi: 10.7717/peerj.9315. eCollection 2020.
Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. and are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of and one each of from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within was striking, resulting in major shifts and independent gene losses. Specifically, was lost independently in the complex and in , with a further loss of and a major contraction of the inverted repeat in two accessions of the latter. represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.
质体基因组（质体基因组）是系统发育基因组学丰富的信息来源，可用于从高级研究到物种以下水平的研究。漆树属已从系统发育和生物地理学角度受到大量研究，但该属的基因组研究仍很缺乏。柔毛漆和加州漆是美国西南部和墨西哥具有重要生态意义的两种灌木物种，它们占据沿海灌丛和矮橡树林栖息地。它们频繁杂交，代表了一个研究杂交和趋异选择相反作用的迷人系统，但从基因组角度来看，其特征尚不明确。在本研究中，对柔毛漆的一个种质以及来自加利福尼亚州和亚利桑那州的各一个加州漆种质进行了完整质体基因组测序。对这三个种质之间的序列变异进行了表征，并设计了可能用于系统地理学研究的PCR引物。基于一个强大支持的系统发育框架进行了系统发育基因组分析——该框架基于无患子目52个完整质体基因组构建。当用系统发育最小二乘回归分析时，重复序列含量而非反向重复序列的大小与整个无患子目质体基因组总长度有更强的相对关联。柔毛漆内反向重复序列边界处的变异很显著，导致了重大变化和独立的基因丢失。具体而言，在柔毛漆复合体和加州漆中分别独立丢失了rpl2，后者的两个种质中还进一步丢失了rps19并出现反向重复序列的重大收缩。柔毛漆代表了一个在物种水平及以下研究光合被子植物质体基因组结构变异的有前景的新系统。
