AUTHOR=Wang Rong , Liu Kuan , Zhang Xue-Jie , Chen Wen-Li , Qu Xiao-Jian , Fan Shou-Jin 

TITLE=Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.638597

DOI=10.3389/fpls.2021.638597

ISSN=1664-462X

ABSTRACT=<p><italic>Cleistogenes</italic> (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of <italic>Cleistogenes</italic> and phylogenetic relationships among <italic>Cleistogenes</italic> taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of <italic>Cleistogenes</italic>, the plastomes of 12 <italic>Cleistogenes</italic> taxa (including 8 species and 4 varieties), one <italic>Orinus</italic> species, 15 <italic>Triodia</italic> species, two <italic>Tripogon</italic> species, and two <italic>Aeluropus</italic> species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (<italic>O. kokonorica</italic>) to 161 (<italic>T. plurinervata</italic> and <italic>T. schinzii</italic>). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (<italic>T. stipoides</italic>) to 16,678 (<italic>T. tomentosa</italic>) codons. Sequence divergence analysis among <italic>Cleistogenes</italic> and closely related genera identified five non-coding regions (<italic>trnS-UGA-psbZ</italic>, <italic>rpl32-trnL-UAG</italic>, <italic>trnQ-UUG-psbK</italic>, <italic>trnD-GUC-psbM</italic>, <italic>trnT-GGU-trnE-UUC</italic>). Phylogenetic analysis of complete plastomes indicated that <italic>Cleistogenes</italic> is sister to a clade composed of <italic>Orinus</italic> and <italic>Triodia</italic>, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (<italic>Cleistogenes</italic> and <italic>Orinus</italic>) and <italic>Triodia</italic>. The subtribe Orininae was not supported by our complete plastome data. The split between <italic>Cleistogenes</italic> and <italic>Orinus</italic>-<italic>Triodia</italic> clade go back to 14.01 Ma. Besides, our findings suggested that <italic>C. squarrosa</italic> and <italic>C. songorica</italic> are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of <italic>Cleistogenes</italic> sp. nov. and <italic>C. caespitosa</italic> var. <italic>ramosa</italic> is sister to other eight <italic>Cleistogenes</italic> taxa. <italic>Cleistogenes</italic> was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within <italic>Cleistogenes</italic>. Collectively, our results provided valuable insights into the phylogenetic study of grass species.</p>