Plastome structure, evolution, and phylogeny of Selaginella
Plastome structure, evolution, and phylogeny of Selaginella
复制标题
卷柏的质体结构、进化和系统发育
DOI：
10.1016/j.ympev.2022.107410
复制
发表时间：
2022
影响因子：
4.1
通讯作者：
Li-Bing Zhang
中科院分区：
文献类型：
--
作者：
Xin-Mao Zhou;Jing Zhao;Jian-Jun Yang;Timothée Le Péchon;Liang Zhang;Zhao-Rong He;Li-Bing Zhang
卷柏作为最早的陆生植物谱系之一，对研究陆生植物的进化具有重要意义。它是石松植物中最大的属，有700-800种。据报道，卷柏的一些独特的性状，但仅基于20种。在相对较大的样本基础上，尚无卷柏的质体体系统发育，在小数据集的基础上，也没有对神秘的sinensis类群的系统发育进行解决，其关系尚不清楚。本文对卷柏属6个亚属51个种的59个质体的结构进行了研究，其中除2个亚属外，还首次纳入了sinensis类群。主要结果包括：(1)卷柏的质体体大小在78,492 bp ~ 187,632 bp之间变化很大；(2)与其他石松植物Isoëtaceae和石松科相比，卷柏树存在大量的基因缺失；(3)卷柏树系和所有半系类群的基因含量和质体结构在质体组系统发育中得到了很好的支持；(4)具有DR结构且没有其他短重复序列或中等重复序列的物种，其endhgene家族容易丢失或假原化；(5) SC短重复区和中重复区介导多种构象，形成多样复杂的质体结构，并发现了6种新的构象；(6) 48种样品具有高GC含量（约50%），但三种sinensis组的质体中GC含量为~ 30%，与大多数维管植物相似；(7)三叶草类群是单系的，包括至少两个亚类群，除了一些寄生植物外，它们的质体是陆地植物中最小的，并且它们的质体不含任何trna；(8)卷叶系较年轻系GC含量较高，较老系GC含量较低；(9)由于基因组数据不完整、结构异常或一些未知的原因，即使是连接的质体也不能很好地确定卷柏树的系统发育关系，突出了解决这一特别重要的陆地植物谱系的系统发育和进化问题的难度。
As one of the earliest land plant lineages,Selaginellais important for studying land plant evolution. It is the largest genus of lycophytes containing 700–800 species. Some unique characters ofSelaginellaplastomes have been reported, but based only on 20 species. There have been no plastome phylogenies ofSelaginellabased on a relatively large sampling, and no efforts have been made to resolve the phylogeny of the enigmaticSinensisgroup whose relationships have been unclear based on small datasets. Here we investigated the structures of 59 plastomes representing 51 species covering all six subgenera and 18 sections ofSelaginellaexcept two sections and including the intriguingSinensisgroup for the first time. Our major results include: (1) the plastome size ofSelaginellaranges tremendously from 78,492 bp to 187,632 bp; (2) there are numerous gene losses inSelaginellacomparing with other lycophytes, Isoëtaceae and Lycopodiaceae; (3) the gene contents and plastome structures inSelaginellavary lineage-specifically and all infrageneric taxa are well supported in the plastome phylogeny; (4) thendhgene family tends to lose or pseudogenize in those species with DR structure and without other short or medium repeats; (5) the short and medium repeat regions in SC mediate many conformations causing diverse and complex plastome structures, and six new conformations are discovered; (6) forty-eight species sampled have high GC content (>50%) but three species in theSinensisgroup have ∼ 30% GC content in plastomes, similar to most vascular plants; (7) theSinensisgroup is monophyletic, includes at least two subgroups, and has the smallest plastomes in land plants except some parasitic plants, and their plastomes do not contain any tRNAs; (8) the younger lineages inSelaginellatend to have higher GC content, whereas the older lineages tend to have lower GC content; and (9) because of incomplete genomic data and abnormal structures or some unknown reasons, even the concatenated plastomes could not well resolve the phylogenetic relationships inSelaginellawith confidence, highlighting the difficulty in resolving the phylogeny and evolution of this particularly important land plant lineage.