Guo Xian-Lin, Xie Fu-Min, Wang Chao-Jie, Ding Yi-Hang, Yan Wen-Chao, Fang Kai, Chen Huai
CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 23, Qunxian South Street, Tianfu New Area, Chengdu, 610213, China.
Sichuan Provincial Institute of Forestry and Grassland Inventory and Planning, Chengdu, 610081, China.
BMC Genomics. 2025 Jul 1;26(1):585. doi: 10.1186/s12864-025-11763-y.
Sphagnum L. (peat mosses) comprises approximately 291 recognized species distributed worldwide except Antarctica. Plastomes are useful for investigating structure evolution and phylogeny due to their conserved structure. However, Sphagnum species endemic to China have been underrepresented in plastome-based studies, hindering a comprehensive understanding of their evolutionary history.
Analysis of 13 plastomes of eight Sphagnum species from China, revealed both inter-and intraspecific variations. Plastome sizes ranged from 138,958 bp (S. acutifolioides) to 141,257 bp (S. ovatum), with conserved gene content (86 CDSs, 37 tRNAs, 8 rRNAs). All plastomes exhibited a typical quadripartite structure: LSC (96,896-99,205 bp), SSC (21,187-21,381 bp), and IRs (10,298-10,391 bp). The IR boundaries and adjacent genes were consistent, except in S. squarrosum, where chIL entered IRb and ndhF entered IRa. Premature termination of the petN gene was detected in all species except S. medium and S. palustre (population: GZ and HB). Codons with RSCU > 1.00 favored A/U at the third position, with UUA (Leucine) and GCU (Alanine) being most common. SSRs dominated by mono- and di-repeats, with tri-repeats were highly conserved. Phylogenetic analysis supported the placement of S. ovatum, S. subsecundum, and S. acutifolioides in subgenus Subsecunda; S. medium and S. palustre in subgenus Sphagnum; and S. warnstorfii, S. fuscum, and S. squarrosum in subgenus Acutifolia.
Despite overall structural conservation, expanded sampling revealed both inter- and intraspecific plastome variation in Sphagnum, underscoring the utility of plastomes for phylogenetic inference and assessing genetic diversity. These findings enhance our understanding of Chinese Sphagnum species and their evolutionary relationships.
泥炭藓属（Sphagnum L.）包含约291个已确认的物种，分布于除南极洲以外的世界各地。质体基因组由于其结构保守，对于研究结构进化和系统发育很有用。然而，基于质体基因组的研究中，中国特有的泥炭藓物种代表性不足，这阻碍了对其进化历史的全面理解。
对来自中国的8种泥炭藓的13个质体基因组进行分析，揭示了种间和种内变异。质体基因组大小从138,958 bp（尖叶泥炭藓S. acutifolioides）到141,257 bp（卵叶泥炭藓S. ovatum）不等，基因含量保守（86个编码序列、37个tRNA、8个rRNA）。所有质体基因组均呈现典型的四分体结构：大单拷贝区（LSC，96,896 - 99,205 bp）、小单拷贝区（SSC，21,187 - 21,381 bp）和反向重复区（IRs，10,298 - 10,391 bp）。IR边界和相邻基因是一致的，但粗叶泥炭藓（S. squarrosum）除外，其叶绿体反向重复区b（chIL）进入IRb，ndhF进入IRa。除中位泥炭藓（S. medium）和泥炭藓（S. palustre，种群：GZ和HB）外，所有物种均检测到petN基因的提前终止。相对同义密码子使用度（RSCU）> 1.00的密码子在第三位偏好A/U，其中UUA（亮氨酸）和GCU（丙氨酸）最为常见。简单序列重复（SSRs）以单拷贝和双拷贝为主，三拷贝高度保守。系统发育分析支持卵叶泥炭藓、偏叶泥炭藓和尖叶泥炭藓归入偏叶泥炭藓亚属（Subsecunda）；中位泥炭藓和泥炭藓归入泥炭藓亚属（Sphagnum）；以及暖地泥炭藓、fuscum泥炭藓和粗叶泥炭藓归入尖叶泥炭藓亚属（Acutifolia）。
尽管总体结构保守，但扩大样本量揭示了泥炭藓质体基因组的种间和种内变异，强调了质体基因组在系统发育推断和评估遗传多样性方面的实用性。这些发现增进了我们对中国泥炭藓物种及其进化关系的理解。
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