The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes
The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes
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DOI：
10.1111/tpj.15351
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发表时间：
2021-06-13
期刊：
影响因子：
7.2
通讯作者：
Ruhlman, Tracey A.
中科院分区：
文献类型：
--
作者：
Lee, Chaehee;Choi, In-Su;Ruhlman, Tracey A.
质体基因组（plastome），而令人惊讶的是，在大多数光合被子植物的基因顺序和内容的恒定，表现出在几个不相关的谱系变异。在豆科植物的多样化发展过程中，质体经历了许多重排，包括反转、扩增、收缩和典型的反向重复序列（IR）的丢失、基因丢失和重复序列积累等。虽然豆类塑性体已经成为研究的主题一段时间，但大多数工作都集中在缺乏IR的分支（IRLC）和植物模式苜蓿（Medicago truncatula）中的农业物种上。凤蝶亚科，其中包含几乎所有的农业豆类物种，也包括大部分的质体变异，迄今为止在家庭中检测到。在这项研究中，三个非蝶状体包括在34个新测序的豆科植物质体，沿着与33个公开可用的序列，以评估在亚科质体结构进化。在努力检查plastome变化的亚科，约20%的采样代表IRLC与其余的选择代表早期分支的papiliperidae分支。一些IR相关的和重复介导的变化进行了鉴定，并在系统发育的背景下进行了检查。与ycf2相关的直接重复序列之间的重组导致个体内质体异质性。虽然损失的IR还没有报道在豆科植物以外的IRLC，一个genistoid分类群被发现完全缺乏典型的质体IR。的IR和非IR重复的质体变化的进展中的作用进行了讨论。
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.