类车前植物（车前科）的质体基因组揭示了属间结构的并系同源现象和车前属的局部超突变以及 Littorella 中 ndh 基因的功能丧失。

Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella.

机构信息

Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA.

Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA.

出版信息

Mol Phylogenet Evol. 2021 Sep;162:107217. doi: 10.1016/j.ympev.2021.107217. Epub 2021 Jun 1.

DOI:10.1016/j.ympev.2021.107217

PMID:34082129

Abstract

Tribe Plantagineae (Plantaginaceae) comprises ~ 270 species in three currently recognized genera (Aragoa, Littorella, Plantago), of which Plantago is most speciose. Plantago plastomes exhibit several atypical features including large inversions, expansions of the inverted repeat, increased repetitiveness, intron losses, and gene-specific increases in substitution rate, but the prevalence of these plastid features among species and subgenera is unknown. To assess phylogenetic relationships and plastomic evolutionary dynamics among Plantagineae genera and Plantago subgenera, we generated 25 complete plastome sequences and compared them with existing plastome sequences from Plantaginaceae. Using whole plastome and partitioned alignments, our phylogenomic analyses provided strong support for relationships among major Plantagineae lineages. General plastid features-including size, GC content, intron content, and indels-provided additional support that reinforced major Plantagineae subdivisions. Plastomes from Plantago subgenera Plantago and Coronopus have synapomorphic expansions and inversions affecting the size and gene order of the inverted repeats, and particular genes near the inversion breakpoints exhibit accelerated nucleotide substitution rates, suggesting localized hypermutation associated with rearrangements. The Littorella plastome lacks functional copies of ndh genes, which may be related to an amphibious lifestyle and partial reliance on CAM photosynthesis.

摘要

车前草族（车前科）由三个目前公认的属（Aragoa、Littorella、Plantago）组成，约有 270 种，其中以车前属最为丰富。车前草质体基因组具有几个非典型特征，包括大的倒位、反向重复的扩展、重复序列的增加、内含子的丢失以及基因特异性取代率的增加，但这些质体特征在物种和亚属中的普遍性尚不清楚。为了评估车前草族属和车前草亚属之间的系统发育关系和质体进化动态，我们生成了 25 个完整的质体序列，并将其与来自车前科的现有质体序列进行了比较。通过全质体和分区比对，我们的系统基因组分析为车前草族主要谱系之间的关系提供了强有力的支持。一般的质体特征——包括大小、GC 含量、内含子含量和插入缺失——提供了额外的支持，加强了车前草族的主要分支。来自车前草亚属 Plantago 和 Coronopus 的质体具有共有的扩张和倒位，影响了反向重复的大小和基因顺序，而在倒位断点附近的特定基因则表现出加速的核苷酸取代率，这表明与重排相关的局部超突变。Littorella 质体缺乏 ndh 基因的功能拷贝，这可能与两栖生活方式和部分依赖 CAM 光合作用有关。