The Ohio State University Museum of Biological Diversity, Department of Evolution, Ecology, and Organismal Biology, Columbus, Ohio 43212, USA.
West Virginia University, Department of Biology, Morgantown, West Virginia 26505, USA.
Am J Bot. 2018 Jan;105(1):71-84. doi: 10.1002/ajb2.1001. Epub 2018 Feb 12.
As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes).
Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum. Sequenced plastomes were compared in a phylogenetic context provided by maximum likelihood and parsimony inferences made using an additional 18 publicly available plastomes from early-diverging angiosperm lineages.
In contrast to previously published magnoliid plastomes and the newly sequenced Saruma henryi plastome published here, Asarum plastomes have undergone extensive disruption and contain extremely lengthy AT-repeat regions. The entirety of the small single copy region (SSC) of A. canadense and A. sieboldii var. sieboldii has been incorporated into the inverted repeat regions (IR), and the SSC of A. delavayi is only 14 bp long. All sampled Asarum plastomes share an inversion of a large portion of the large single copy region (LSC) such that trnE-UUC is adjacent to the LSC-IR boundary.
Plastome divergence in Asarum appears to be consistent with trends seen in highly rearranged plastomes of the monocots and eudicots. We propose that plastome instability in Asarum is due to repetitive motifs that serve as recombinatory substrates and reduce genome stability.
随着越来越多的质体基因组被组装，很明显，重排、缺失、基因间间隔区的扩张和收缩以及功能正常的质体之间的同线性断裂比之前想象的更为常见，而且这些变化在不同的谱系中是独立发展的。然而，迄今为止，木兰类植物的质体基因组（质体基因组）仍然以高度保守为特征。
使用 Illumina HiSeq 和 MiSeq 平台对 Saruma henryi 的质体基因组以及来自 Asarum 六个分类群代表物种的质体基因组进行测序。在最大似然法和简约法推断的系统发育背景下比较测序质体基因组，使用来自早期分化的被子植物谱系的另外 18 个公开的质体基因组进行推断。
与之前发表的木兰类质体基因组和这里新发表的 Saruma henryi 质体基因组相比，Asarum 质体基因组发生了广泛的破坏，并且含有非常长的 AT 重复区。A. canadense 和 A. sieboldii var. sieboldii 的小单拷贝区（SSC）的全部都已整合到反向重复区（IR）中，而 A. delavayi 的 SSC 只有 14 bp 长。所有被采样的 Asarum 质体基因组都共享一个大单拷贝区（LSC）的大部分倒位，使得 trnE-UUC 与 LSC-IR 边界相邻。
Asarum 质体基因组的分化似乎与单子叶植物和真双子叶植物高度重排质体基因组中观察到的趋势一致。我们提出，Asarum 质体基因组的不稳定性是由于重复基序作为重组底物，降低了基因组的稳定性。
