Complete Chloroplast Genome Structural Characterization of Paludella squarrosa and Comparative Analysis
with Its Alliance

doi:10.3969/j.issn.1009-7791.2025.02.002

Subtropical Plant Science ›› 2025, Vol. 54 ›› Issue (2): 121-131.DOI: 10.3969/j.issn.1009-7791.2025.02.002

• Research articles • Previous Articles Next Articles

Complete Chloroplast Genome Structural Characterization of Paludella squarrosa and Comparative Analysis with Its Alliance

HUANG Ding-xu¹, MA Huai-fu², LIANG Sheng¹, HE Qin-qin¹, ZHANG Ting-yue¹, KONG Ling-xiong¹, LIU Bang-you¹, KANG Kai-li², PENG Tao^2*

(1. Guizhou Chishui Alsophila National Nature Reserve, Chishui 564700, Guizhou China; 2. School of Life Sciences, Guizhou Normal University, Guiyang 550025, Guizhou China)

Received:2024-12-05 Accepted:2025-01-14 Online:2025-04-30 Published:2025-06-27
Contact: PENG Tao

沼寒藓叶绿体基因组结构特征及其与近缘物种比较

黄定旭¹，马怀富²，梁盛¹，何琴琴¹，张廷跃¹，孔令雄¹，刘邦友¹，康凯莉²，彭涛^2*

(1. 贵州赤水桫椤国家级自然保护区管理局，贵州赤水 564700；2. 贵州师范大学生命科学学院，贵州贵阳 550025)

通讯作者: 彭涛
基金资助:
赤水桫椤国家级自然保护区药用植物调查项目

Abstract

Abstract: Paludella squarrosa is primarily distributed in wetland environments and is one of the key bryophyte species in wetland ecosystems, playing a unique role in wetland ecology and plant evolutionary studies. In this study, the chloroplast genome of P. squarrosa was assembled and annotated using Illumina next-generation sequencing technology, and its basic features were analyzed. The results showed that the chloroplast genome of P. squarrosa is 124 879 bp in size, containing a large single-copy region (LSC, 86 458 bp), a small single-copy region (SSC, 18 529 bp), and two inverted repeat regions (IRa and IRb, both 9946 bp), with a GC content of 28.9%. The genome contains 122 genes, including 77 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Sequence analysis revealed 49 dispersed repeat sequences, predominantly palindromic repeats, and identified seventeentypes of simple sequence repeats (SSRs), with A/T repeats being the most common. Additionally, comparative genomic analysis with species of the order Splachnales from GenBank revealed high similarity between P. squarrosa and Tayloria sp. in genome size, gene content, and sequence composition. Phylogenetic analysis based on the rps4 and trnL-F genes indicated that P. squarrosa is closely related to Amblyodon dealbatus. As a representative species of Meesiaceae, the chloroplast genome study of P. squarrosa provides new insights into the evolutionary history, genomic characteristics, and ecological adaptation mechanisms of Meesiaceae plants.

Key words: Paludella squarrosa, chloroplast genome, phylogenetic analysis, comparative genomics

摘要： 沼寒藓Paludella squarrosa主要分布于湿地环境，是湿地生态系统中重要的苔藓植物之一，在湿地生态学和植物进化学研究中具有独特的地位。采用Illumina二代测序技术对沼寒藓的叶绿体基因组进行组装与注释，并对其基本特征进行分析。结果表明，沼寒藓叶绿体基因组大小为124 879 bp，包含大单拷贝区(LSC，86 458 bp)、小单拷贝区(SSC，18 529 bp)及两个反向重复序列(IRa和IRb，均为9 946 bp)，基因组GC含量为28.9%。该基因组共包含122个基因，其中77个为编码蛋白质基因，8个为编码rRNA基因，37个为编码tRNA基因。序列分析发现四种散在重复序列共49个，其中以回文重复序列为主；并鉴定出17种类型的SSR，其中以单核苷酸(A/T)重复为主。同时，选取GenBank中壶藓目Splachnales物种进行比较基因组学分析，发现沼寒藓与Tayloria sp.在基因组大小、基因含量和序列上高度相似。基于rps4和trnL-F基因的系统发育分析表明，沼寒藓与Amblyodon dealbatus的亲缘关系较近。作为寒藓科Meesiaceae的代表性物种，沼寒藓的叶绿体基因组研究为深入理解寒藓科植物的进化历史、基因组特征以及生态适应机制提供新的视角。

关键词: 沼寒藓, 叶绿体基因组, 基因组特征, 系统发育

CLC Number:

Q949

HUANG Ding-xu, MA Huai-fu, LIANG Sheng, HE Qin-qin, ZHANG Ting-yue, KONG Ling-xiong, LIU Bang-you, KANG Kai-li, PENG Tao. Complete Chloroplast Genome Structural Characterization of Paludella squarrosa and Comparative Analysis with Its Alliance[J]. Subtropical Plant Science, 2025, 54(2): 121-131.

黄定旭, 马怀富, 梁盛, 何琴琴, 张廷跃, 孔令雄, 刘邦友, 康凯莉, 彭涛. 沼寒藓叶绿体基因组结构特征及其与近缘物种比较[J]. 亚热带植物科学, 2025, 54(2): 121-131.

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Complete Chloroplast Genome Structural Characterization of Paludella squarrosa and Comparative Analysis with Its Alliance

沼寒藓叶绿体基因组结构特征及其与近缘物种比较

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