多腺拟蝶唇兰质体基因组特征及其系统发育分析

XU Jing; PAN Ren-fu; HUANG Si-ming; HUANG Wei-chang; LI Ming-he

doi:10.3969/j.issn.1009-7791.2025.05.001

亚热带植物科学 >

2025 , Vol. 54 >Issue 5: 487 - 496

DOI: https://doi.org/10.3969/j.issn.1009-7791.2025.05.001

研究论文

多腺拟蝶唇兰质体基因组特征及其系统发育分析

XU Jing ,
PAN Ren-fu ,
HUANG Si-ming ,
HUANG Wei-chang ,
LI Ming-he

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(1. 福建农林大学风景园林与艺术学院，福建福州 350108；2. 上海辰山植物园华东野生濒危资源植物保育中心，上海 201602)

收稿日期: 2025-03-29

录用日期: 2025-04-22

网络出版日期: 2025-12-17

基金资助

国家自然科学基金项目(32271957)

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Plastid Genome and Phylogenetic Analysis of Psychopsis sanderae

许静，潘仁富，黄思铭，黄卫昌，李明河

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(1. College of Landscape and Art, Fujian Agriculture and Forestry University, Fuzhou 350108, Fujian China; 2. Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China)

Received date: 2025-03-29

Accepted date: 2025-04-22

Online published: 2025-12-17

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摘要

以观赏兰科植物多腺拟蝶唇兰Psychopsis sanderae叶片为材料，基于高通量测序技术，对该物种完整的质体基因组进行组装和注释，并解析其质体基因组特征及系统发育位置。结果表明，多腺拟蝶唇兰质体基因组大小为143 932 bp，呈环状四分体结构，GC含量37.1%；共注释到蛋白编码基因74个、tRNA基因38个、rRNA基因8个和假基因7个，共计127个，其中ndh基因家族全谱系假基因化或丢失；IR区边界高度保守，LSC/IRb位于rpl22基因内，SSC/IRa位于ycf1基因内；检测到44个简单重复序列位点，其中以A或T单核苷酸重复最高，占70.45%；获得核苷酸多态性的高变异热点区域6个：trnQUUG、trnEUUC、trnSGGA、rps18、rps12、rpl16。系统发育分析显示，该物种位于文心兰亚族Oncidiinae基部。本研究首次解析多腺拟蝶唇兰质体基因组特征，为拟蝶唇兰属及其近缘类群的分子标记开发和系统发育研究奠定基础。

关键词： 多腺拟蝶唇兰; 质体基因组; 分子系统发育; 文心兰亚族

本文引用格式

XU Jing , PAN Ren-fu , HUANG Si-ming , HUANG Wei-chang , LI Ming-he . 多腺拟蝶唇兰质体基因组特征及其系统发育分析[J]. 亚热带植物科学, 2025 , 54(5) : 487 -496 . DOI: 10.3969/j.issn.1009-7791.2025.05.001

Abstract

Using the leaves of the ornamental orchid Psychopsis sanderae as materials, based on high-throughput sequencing technology, the complete plastid genome of this species was assembled and annotated, and its plastid genome characteristics and phylogenetic position were analyzed. The results showed that the plastid genome of P. sanderae was 143 932 bp in size, presenting a circular quadripartite structure, with a GC content of 37.1%. A total of 127 genes were annotated, including 74 protein-coding genes, 38 transfer RNAs (tRNAs) genes, 8 ribosomal RNAs (rRNAs) genes and 7 pseudo genes. Among them, the entire lineage of the ndh gene family was pseudogenized or lost. The boundaries of the inverted repeat (IR) regions were highly conserved. The junction of the large single copy (LSC) region and the IRb region was located within the rpl22 gene, and the junction of the small single copy (SSC) region and the IRa region was located within the ycf1 gene. A total of 44 simple sequence repeats (SSRs) loci were detected, among which the mononucleotide repeats with adenine (A) or thymine (T) were the most abundant, accounting for 70.45%. Six high-variation hotspots of nucleotide polymorphism were obtained: trnQUUG, trnEUUC, trnSGGA, rps18, rps12, and rpl16. Phylogenetic analyses placed P. sanderae at the basal position within the subtribe Oncidiinae. This study provides the first comprehensive characterization of the plastid genome for P. sanderae, laying a foundation for future molecular marker development and phylogenetic studies of Psychopsis and its relatives.

Key words： Psychopsis sanderae; plastid genome; phylogenetic analysis; Oncidiinae

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