Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.
Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.
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DOI：
10.7717/peerj.9315
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发表时间：
2020-06-16
期刊：
影响因子：
2.7
通讯作者：
Barrett, Craig F.
中科院分区：
文献类型：
--
作者：
Barrett, Craig F.
质体基因组（plastomes）代表了丰富的信息来源，从更高层次的研究，低于物种水平的基因组学。漆树属植物的系统发育和地理分布研究已取得了很大的进展，但基因组学研究还很缺乏。全缘叶盐肤木（Rhus integrifolia）和R.卵形树是两种在美国西南部和墨西哥具有高度生态重要性的灌木状物种，在那里它们占据沿海灌木丛和查帕拉尔栖息地。它们经常杂交，代表了一个迷人的系统，在其中研究杂交和趋异选择的相反影响，但从基因组的角度来看，其特征很差。在这项研究中，完整的质体基因组测序的一个登记R。integrifolia和R.产于加州和亚利桑那州的卵圆花。分析了这3份材料的序列差异，并设计了可用于植物地理学研究的PCR引物。系统基因组学分析进行了强有力的支持系统发育框架的基础上，52个完整的质体横跨无患子目。重复的内容，而不是反向重复的大小，有一个更强的相对关联与总质体长度与系统发育最小二乘回归分析时，无患子目。在盐肤木内的反向重复边界的变化是惊人的，导致重大转变和独立的基因丢失。具体而言，rps 19在R. integrifolia-ovata复合体中，R. chinensis的rps 22进一步丢失，后者的两份材料的反向重复序列显著收缩。盐肤木是一个很有前途的新系统，研究光合被子植物的质体结构变异在种和以下的水平。
Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata 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 R. integrifolia and one each of R. ovata 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 Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.