Huang Lan, Wen Jun, Crabbe M James C, Chen Chiqing, Ren Zhumei
School of Life Science, Shanxi University, Taiyuan, Shanxi, 030006, China.
Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, U.S.A.
Genetica. 2024 Dec 2;153(1):6. doi: 10.1007/s10709-024-00217-0.
The taxonomic concepts and phylogenetic relations among genera of the family Mniaceae have given rise to much controversy in recent years, including Mnium, Plagiomnium, and Pohlia. Chloroplast genome study of these genera will be helpful to reflect the fact of this relationship. In this study, we sequenced three species in the Plagiomnium genus using an Illumina HiSeq 4000 platform. The complete chloroplast genomes of P. rostratum, P. succulentum and P. vesicatum were 125,196 bp, 124,689 bp, and 124,663 bp in length, which all contained a quadripartite structure including two copies of the invert repeats (IR, 10,120 bp, 9,818 bp, and 9,665 bp), one large single copy region (LSC, 86,395 bp, 86,299 bp, and 86,532 bp), and one single copy region (SSC, 18,561 bp, 18,754 bp, and 18,801 bp). The overall GC contents were 29.8%, 30.5%, and 30.5% respectively. The simple sequence repeats (SSRs) were detected in conjunction with Plagiomnium acutum, with variable sites genes observed: rpoC2, ycf1, and ycf2. Combined with the other three sequences published in Mniaceae, analyses of codon usage, repeats sequences, GC contents, and gene features revealed similarities among the seven species in Mniaceae. The trend of nucleotide diversity (Pi) in the seven complete chloroplast genomes showed Pi > 0.056: trnI-rpl23, petG-petL-psbE, trnK-chlB, trnG-trnR-atpA, rpoB-trnC-ycf66, ndhB, trnN-ndhF, and rps15-ycf1. We confirmed the phylogenetic relationships that Plagiomnium genus is a sister group with Mnium, while the Pohlia genus is not a monophyletic group. Phylogenetic analyses corroborated the monophyly of Mniaceae and supported the transfer of the Pohlia genus into Mniaceae.
近年来，藓科各属之间的分类学概念和系统发育关系引发了诸多争议，其中包括提灯藓属、匍灯藓属和丝瓜藓属。对这些属进行叶绿体基因组研究将有助于揭示这种关系的实际情况。在本研究中，我们使用Illumina HiSeq 4000平台对匍灯藓属的三个物种进行了测序。钝叶匍灯藓、湿地匍灯藓和具瘤匍灯藓的完整叶绿体基因组长度分别为125,196 bp、124,689 bp和124,663 bp，均具有四分体结构，包括两个反向重复序列（IR，分别为10,120 bp、9,818 bp和9,665 bp）、一个大单拷贝区域（LSC，分别为86,395 bp、86,299 bp和86,532 bp）和一个单拷贝区域（SSC，分别为18,561 bp、18,754 bp和18,801 bp）。总体GC含量分别为29.8%、30.5%和30.5%。结合尖叶匍灯藓检测到了简单序列重复（SSR），观察到了可变位点基因：rpoC2、ycf1和ycf2。结合藓科已发表的其他三个序列，对密码子使用、重复序列、GC含量和基因特征进行分析，揭示了藓科七个物种之间的相似性。七个完整叶绿体基因组中核苷酸多样性（Pi）的趋势显示Pi > 0.056的区域为：trnI-rpl23、petG-petL-psbE、trnK-chlB、trnG-trnR-atpA、rpoB-trnC-ycf66、ndhB、trnN-ndhF和rps15-ycf1。我们确认了系统发育关系，即匍灯藓属是提灯藓属的姐妹群，而丝瓜藓属不是一个单系类群。系统发育分析证实了藓科的单系性，并支持将丝瓜藓属归入藓科。
