Comparative Analysis of Chloroplast Genomes of Allium Species

doi:10.11733/j.issn.1007-0435.2025.12.006

Acta Agrestia Sinica ›› 2025, Vol. 33 ›› Issue (12): 3920-3932.DOI: 10.11733/j.issn.1007-0435.2025.12.006

• 2025-12-28 • Previous Articles

Comparative Analysis of Chloroplast Genomes of Allium Species

GUO Ming-yan, MA Hai-xia, QIAO Tian-le, YIN Yu, WANG Xin-wei, LI Jin-ming, FENG Shuo

State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province 810016, China

Received:2025-01-02 Revised:2025-02-27 Published:2025-12-01

葱属植物叶绿体基因组比较分析

郭铭炎, 马海霞, 乔天乐, 殷钰, 王欣维, 李金洺, 封烁

青海大学省部共建三江源生态与高原农牧业国家重点实验室, 青海西宁 810016

通讯作者: 封烁，E-mail：fengshuo8894@126.com
作者简介:郭铭炎（2003-），女，汉族，河南平顶山人，本科生，E-mail：3437951548@qq.com；
基金资助:
青海省“帅才科学家”负责制项目（2024-SF-102）资助

Abstract

Abstract: The genus Allium L. belongs to the family Amaryllidaceae and comprises more than 900 species with significant economic and medicinal values. To elucidate the chloroplast genome characteristics of Allium species and conduct molecular markers for Allium species， this study assembled and annotated the chloroplast genome of A. tuberosum Rottler ex Sprengle. using high-throughput sequencing technology and compared it with six closely related species， including： A. cepa L.， A. galanthum Kar. & Kir.， A. chrysanthum Regel.， A. altaicum Pall.， A. fistulosum L.， and A. schoenoprasum L. Through simple sequence repeat （SSR） analysis， codon usage bias analysis， inverted repeat boundary analysis， collinearity analysis， and phylogenetic analysis， the results showed that the chloroplast genomes of the seven species ranged from 152 852 to 154 056 bp in length， with a GC content of 37% and a typical quadripartite structure. A total of 73 to 99 SSRs were detected， predominantly consisting of mononucleotide repeats （A/T types）. Notably， a unique hexanucleotide repeat sequence （AAAAAT/ATTTTT） of A. tuberosum is inferred to be associated with the localization of coding sequence （CDS） and gene expression regulation. Additionally， the chloroplast genomes of Allium species were generally conserved， but significant differences were observed in the boundaries between the inverted repeat b （IRb） and small single-copy （SSC） regions. A. tuberosum is found to be more closely related to A. chrysanthum， but distantly related to A. altaicum. This study provides important references for research on the genetic diversity， specific gene mining， and phylogenetic relationships of the genus Allium.

Key words: Allium, Chloroplast genome, Simple sequence repeat （SSR） analysis, Codon usage bias analysis, Comparative genomics, Phylogenetic analysis

摘要： 葱属（Allium L.）隶属于石蒜科，含900余种，兼具重要经济和药用价值。为解析葱属叶绿体基因组特征及开发分子标记，本研究基于高通量测序技术完成韭菜（Allium tuberosum Rottler ex Sprengle.）叶绿体基因组组装及注释，并与洋葱（Allium cepa L.）、实葶葱（Allium galanthum Kar. & Kir.）、野葱（Allium chrysanthum Regel.）、阿尔泰葱（Allium altaicum Pall.）、葱（Allium fistulosum L.）和糙葶北葱（Allium schoenoprasum L.）6个近缘种进行比较。通过简单重复序列（Simple sequence repeat， SSR）、密码子偏好性、反向重复序列边界、共线性及系统发育分析，结果显示：7种植物叶绿体基因组全长为152 852~154 056 bp，GC含量均为37%，呈典型四分体结构；共检测到73~99个SSRs，以单核苷酸重复（A/T型）为主，韭菜特有的六核苷酸重复序列AAAAAT/ATTTTT推断与编码序列（Coding sequence， CDS）区定位及基因表达调控相关；葱属叶绿体基因组整体保守，但反向重复序列b（Inverted repeat b， IRb）与小单拷贝（Small single-copy， SSC）边界差异较大；韭菜与野葱亲缘关系较近，与阿尔泰葱关系较远。本研究为葱属遗传多样性、特异基因挖掘及系统发育等研究提供了重要参考。

关键词: 葱属, 叶绿体基因组, 简单重复序列分析, 密码子偏好性分析, 比较基因组学, 系统发育分析

CLC Number:

S633

GUO Ming-yan, MA Hai-xia, QIAO Tian-le, YIN Yu, WANG Xin-wei, LI Jin-ming, FENG Shuo. Comparative Analysis of Chloroplast Genomes of Allium Species[J]. Acta Agrestia Sinica, 2025, 33(12): 3920-3932.

郭铭炎, 马海霞, 乔天乐, 殷钰, 王欣维, 李金洺, 封烁. 葱属植物叶绿体基因组比较分析[J]. 草地学报, 2025, 33(12): 3920-3932.

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Comparative Analysis of Chloroplast Genomes of Allium Species

葱属植物叶绿体基因组比较分析

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