Data from: Total duplication of the small single copy region in the angiosperm plastome: rearrangement and inverted repeat instability in Asarum

Premise of the Study: 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).

Methods: 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.

Key Results: 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.

Conclusions: 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.

研究背景：随着越来越多的质体基因组（plastome）被组装完成，现已明确，在正常功能的质体中发生的基因组重排、基因丢失、基因间隔区的扩张与收缩以及共线性断裂，远比此前预想的更为常见，且这类变异在不同的演化支中独立发生。然而截至目前，木兰类植物的质体基因组仍以高度保守为典型特征。
研究方法：本研究采用Illumina HiSeq及MiSeq测序平台，对马蹄香（Saruma henryi）以及细辛属（Asarum）6个组各代表物种的质体基因组进行测序。结合另外18个公开的早期分化被子植物支系的质体基因组数据，通过最大似然法与简约法进行系统发育推断，以此构建系统发育框架，对已测序的质体基因组开展比较分析。
主要结果：与此前已发表的木兰类质体基因组，以及本研究新测序并发表的马蹄香质体基因组不同，细辛属物种的质体基因组发生了广泛的结构重排，并包含极长的AT重复区域。加拿大细辛（A. canadense）与朝鲜细辛原变种（A. sieboldii var. sieboldii）的全部小单拷贝区（small single copy region, SSC）均已整合至反向重复区（inverted repeat regions, IR）中；而滇细辛（A. delavayi）的小单拷贝区长度仅为14 bp。所有被采样的细辛属质体基因组均存在大片段的大单拷贝区（large single copy region, LSC）倒位，使得trnE-UUC基因紧邻LSC-IR边界。
研究结论：细辛属的质体基因组分化趋势，与单子叶植物和真双子叶植物中高度重排的质体基因组所呈现的规律相符。我们推测，细辛属质体基因组的不稳定性源于可作为重组底物的重复基序，这类基序降低了基因组的结构稳定性。