不同产地珊瑚菜叶绿体基因组特征的差异性研究

doi:10.13560/j.cnki.biotech.bull.1985.2025-0005

生物技术通报 ›› 2025, Vol. 41 ›› Issue (6): 229-242.doi: 10.13560/j.cnki.biotech.bull.1985.2025-0005

• 研究报告 • 上一篇

不同产地珊瑚菜叶绿体基因组特征的差异性研究

安昌¹(), 徐文波², 陆琳¹, 李登麟¹, 姚艺新³, 林彦翔⁴, 杨成梓⁴, 秦源¹(), 郑平¹()

^1.福建农林大学海峡联合研究院基因组学研究中心，福州 350000
^2.中国药科大学中药学院，南京 211198
^3.澳门大学中华医药研究院中药质量研究国家重点实验室，中国澳门 999078
^4.福建中医药大学药学院，福州 350122

收稿日期:2025-01-03 出版日期:2025-06-26 发布日期:2025-06-30
通讯作者: 郑平，副教授，硕士生导师，研究方向：多组学分析和组学大数据挖掘；E-mail: zhengping13@mails.ucas.ac.cn
秦源，教授，博士生导师，研究方向：植物生殖发育及海峡特色植物应用；E-mail: yuanqin@fafu.edu.cn
作者简介:安昌，博士研究生，研究方向：药用植物资源学及基因组学；E-mail: ancher0928@163.com
基金资助:
国家自然科学基金项目(32100168);福建中医药大学校管课题(X2023025)

Comparative Analysis of Glehnia littoralis from Different Geographic Regions Based on the Characteristics of Chloroplast Genome

AN Chang¹(), XU Wen-bo², LU Lin¹, LI Deng-lin¹, YAO Yi-xin³, LIN Yan-xiang⁴, YANG Cheng-zi⁴, QIN Yuan¹(), ZHENG Ping¹()

^1.Center for Genomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350000
^2.School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198
^3.State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
^4.College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122

Received:2025-01-03 Published:2025-06-26 Online:2025-06-30

摘要/Abstract

摘要：

目的研究不同产地珊瑚菜（Glehnia littoralis）的叶绿体基因组的特征及其系统发育关系，从细胞器基因组角度揭示珊瑚菜物种内的遗传变异和群体分化，为其新品种选育和种质资源保护提供遗传学基础。方法对产自福建的珊瑚菜叶绿体基因组进行了组装和注释，随后对6个来自不同产地样本的叶绿体基因组进行比较分析，研究其基因组结构、重复序列分布、密码子使用偏好、核苷酸多态性、基因组边界特征以及系统发育关系，探讨不同产地珊瑚菜之间的遗传多样性和适应性进化特征。结果 6个叶绿体基因组均呈典型的双链环状四分体结构，基因组长度为147 445-147 552 bp，GC含量为37.51%-37.52%，结构高度保守。均注释出129个基因，包括85个蛋白编码基因，8个核糖体RNA和36个转运RNA。SSR数量在77-79之间，共包含6种类型，以A/T类型为主。密码子使用分析表明，编码精氨酸的密码子中福建和中国台湾产地的珊瑚菜倾向于使用的CGA，而深圳和浙江产地的珊瑚菜更偏好CGT。基因组边界特征基因具有一定的保守性，差异主要位于JLB和JLA边界。核苷酸多态性分析共检测出24个的多态性区域。系统发育分析表明，产于韩国的珊瑚菜在演化上独立于其他样本，中国台湾产地与其余地区样本分化最早，显示出独特的遗传特征；福建产地随后分化，深圳和浙江样本形成一个小分支。结论不同产地珊瑚菜在叶绿体基因组结构特征保守，但在密码子使用、基因组边界及核苷酸多态性等方面存在一定变异，系统发育分析表明其群体间存在遗传分化，反映了其适应性进化特征。

关键词: 珊瑚菜, 叶绿体基因组, 不同产地, 比较分析

Abstract:

Objective This study aims to investigate the characteristics of chloroplast genomes and their phylogenetic relationships across different populations of Glehnia littoralis, with a focus on revealing genetic variation and population differentiation within the species from the perspective of organelle genomes. The findings provide a genetic basis for the breeding of new varieties and the conservation of germplasm resources. Method The chloroplast genome of G. littoralis from Fujian was assembled and annotated. Subsequently, comparative analysis was conducted on the chloroplast genomes of six samples from different geographic regions, examining genomic structure, distribution of repetitive sequences, codon usage preference, nucleotide polymorphism, genomic boundary features, and phylogenetic relationships. The study explores the genetic diversity and adaptive evolution traits among populations from different regions. Result All six chloroplast genomes had a typical double-stranded circular quadripartite structure, with genome lengths ranging from 147 445 bp to 147 552 bp and GC content ranging from 37.51% to 37.52%, demonstrating high structural conservation. A total of 129 genes were annotated, including 85 protein-coding genes, 8 ribosomal RNA genes, and 36 transfer RNA genes. The number of simple sequence repeats (SSRs) ranged from 77 to 79, consisting of six types, predominantly A/T repeats. Codon usage analysis indicated that G. littoralis from Fujian and Taiwan (China) preferentially utilized the CGA codon for arginine, whereas those from Shenzhen and Zhejiang favored CGT. Genomic boundary genes showed a degree of conservation, with differences primarily occurring at the JLB and JLA boundaries. Nucleotide polymorphism analysis identified 12 polymorphic genes and 12 intergenic polymorphic regions. Phylogenetic analysis revealed that the Korean population of G. littoralis was evolutionarily distinct from all other samples, while the Taiwan population diverged earliest, showing unique genetic characteristics. The Fujian population followed in divergence, while the Shenzhen and Zhejiang samples formed a minor clade. Conclusion The chloroplast genome structure of Glehnia littoralis from different regions presents high conservation; however, variations are observed in codon usage, genome boundary regions, and nucleotide polymorphisms. Phylogenetic analysis reveals genetic differentiation among populations, reflecting their adaptive evolutionary characteristics.

Key words: Glehnia littoralis, chloroplast genome, different geographic regions, comparative analysis

安昌, 徐文波, 陆琳, 李登麟, 姚艺新, 林彦翔, 杨成梓, 秦源, 郑平. 不同产地珊瑚菜叶绿体基因组特征的差异性研究[J]. 生物技术通报, 2025, 41(6): 229-242.

AN Chang, XU Wen-bo, LU Lin, LI Deng-lin, YAO Yi-xin, LIN Yan-xiang, YANG Cheng-zi, QIN Yuan, ZHENG Ping. Comparative Analysis of Glehnia littoralis from Different Geographic Regions Based on the Characteristics of Chloroplast Genome[J]. Biotechnology Bulletin, 2025, 41(6): 229-242.

图/表 9

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登录号 GenBank ID	产地 Distribution	大小 Size （bp）	蛋白编码基因 PCG	转运RNA tRNA	核糖体RNA rRNA	基因数 Genes	GC （%）	长度 Length （bp）
登录号 GenBank ID	产地 Distribution	大小 Size （bp）	蛋白编码基因 PCG	转运RNA tRNA	核糖体RNA rRNA	基因数 Genes	GC （%）	LSC	SSC	IRb/a
KT153022.1	韩国1	147 467	85	36	8	129	37.51	93 493	17 546	18 214
NC_034645.1	韩国2	147 477	85	36	8	129	37.51	93 496	17 555	18 213
OR004233.1	中国台湾	147 445	85	36	8	129	37.52	92 373	17 548	18 762
PQ563254.1	福建	147 493	85	36	8	129	37.51	93 218	17 545	18 365
MH142518.1	深圳	147 552	85	36	8	129	37.51	93 277	17 545	18 365
OQ863734.1	浙江	147 507	85	36	8	129	37.51	93 231	17 546	18 365

登录号 GenBank ID	产地 Distribution	大小 Size （bp）	蛋白编码基因 PCG	转运RNA tRNA	核糖体RNA rRNA	基因数 Genes	GC （%）	长度 Length （bp）
登录号 GenBank ID	产地 Distribution	大小 Size （bp）	蛋白编码基因 PCG	转运RNA tRNA	核糖体RNA rRNA	基因数 Genes	GC （%）	LSC	SSC	IRb/a
KT153022.1	韩国1	147 467	85	36	8	129	37.51	93 493	17 546	18 214
NC_034645.1	韩国2	147 477	85	36	8	129	37.51	93 496	17 555	18 213
OR004233.1	中国台湾	147 445	85	36	8	129	37.52	92 373	17 548	18 762
PQ563254.1	福建	147 493	85	36	8	129	37.51	93 218	17 545	18 365
MH142518.1	深圳	147 552	85	36	8	129	37.51	93 277	17 545	18 365
OQ863734.1	浙江	147 507	85	36	8	129	37.51	93 231	17 546	18 365

氨基酸 Amino acid	密码子 Codon	数量 Count	同义密码子频率 RSCU	氨基酸 Amino acid	密码子 Codon	数量 Count	同义密码子频率 RSCU
Ala	GCA	303-312	1.09	Leu	CTT	426-457	1.27-1.29
Ala	GCC	175-180	0.63	Leu	CTC	124-140	0.37-0.39
Ala	GCG	129-133	0.46-0.47	Leu	CTG	117-133	0.35-0.37
Ala	GCT	504-515	1.81	Lys	AAG	216-266	0.48-0.49
Arg	AGG	113-123	0.6-0.61	Lys	AAA	670-835	1.51-1.52
Arg	CGA	260-284	1.38-1.4	Met	ATG	435-467	1.00
Arg	AGA	309-368	1.66-1.8	Phe	TTT	681-781	1.32-1.35
Arg	CGC	78-81	0.4-0.42	Phe	TTC	351-373	0.65-0.68
Arg	CGG	91-95	0.46-0.49	Pro	CCT	312-338	1.56-1.57
Arg	CGT	266-278	1.36-1.43	Pro	CCG	128-135	0.62-0.64
Asn	AAC	200-235	0.47-0.48	Pro	CCA	207-231	1.04-1.07
Asn	AAT	648-753	1.52-1.53	Pro	CCC	148-163	0.74-0.75
Asp	GAT	619-673	1.60	Ser	AGC	73-85	0.31-0.33
Asp	GAC	154-167	0.40	Ser	AGT	293-321	1.25-1.26
Cys	TGT	155-164	1.53	Ser	TCT	397-428	1.67-1.71
Cys	TGC	47-50	0.47	Ser	TCG	147-165	0.63-0.65
Gin	CAA	512-570	1.49-1.51	Ser	TCA	253-290	1.09-1.14
Gin	CAG	177-185	0.49-0.51	Ser	TCC	230-243	0.95-0.99
Glu	GAA	714-815	1.49-1.51	Thr	ACC	182-198	0.74
Glu	GAG	246-265	0.49-0.51	Thr	ACA	285-320	1.16-1.2
Gly	GGT	469-485	1.34-1.35	Thr	ACG	104-114	0.42-0.43
Gly	GGG	245-253	0.70	Thr	ACT	409-439	1.64-1.67
Gly	GGA	518-542	1.49-1.5	Trp	TGG	339-370	1.00
Gly	GGC	160-168	0.46	Tyr	TAC	139-159	0.39-0.4
His	CAT	353-380	1.51	Tyr	TAT	566-636	1.6-1.61
His	CAC	115-123	0.49	Val	GTA	398-418	1.46
Ile	ATC	298-327	0.56-0.57	Val	GTC	125-134	0.46-0.47
Ile	ATA	506-571	0.96-0.98	Val	GTG	159-167	0.58
Ile	ATT	773-850	1.46-1.47	Val	GTT	409-430	1.50
Leu	TTG	406-435	1.2-1.23	Ter	TAG	12-12	0.69-0.71
Leu	TTA	646-708	1.95-1.97	Ter	TGA	10-11	0.59-0.63
Leu	CTA	269-290	0.8-0.81	Ter	TAA	29-29	1.67-1.71

氨基酸 Amino acid	密码子 Codon	数量 Count	同义密码子频率 RSCU	氨基酸 Amino acid	密码子 Codon	数量 Count	同义密码子频率 RSCU
Ala	GCA	303-312	1.09	Leu	CTT	426-457	1.27-1.29
Ala	GCC	175-180	0.63	Leu	CTC	124-140	0.37-0.39
Ala	GCG	129-133	0.46-0.47	Leu	CTG	117-133	0.35-0.37
Ala	GCT	504-515	1.81	Lys	AAG	216-266	0.48-0.49
Arg	AGG	113-123	0.6-0.61	Lys	AAA	670-835	1.51-1.52
Arg	CGA	260-284	1.38-1.4	Met	ATG	435-467	1.00
Arg	AGA	309-368	1.66-1.8	Phe	TTT	681-781	1.32-1.35
Arg	CGC	78-81	0.4-0.42	Phe	TTC	351-373	0.65-0.68
Arg	CGG	91-95	0.46-0.49	Pro	CCT	312-338	1.56-1.57
Arg	CGT	266-278	1.36-1.43	Pro	CCG	128-135	0.62-0.64
Asn	AAC	200-235	0.47-0.48	Pro	CCA	207-231	1.04-1.07
Asn	AAT	648-753	1.52-1.53	Pro	CCC	148-163	0.74-0.75
Asp	GAT	619-673	1.60	Ser	AGC	73-85	0.31-0.33
Asp	GAC	154-167	0.40	Ser	AGT	293-321	1.25-1.26
Cys	TGT	155-164	1.53	Ser	TCT	397-428	1.67-1.71
Cys	TGC	47-50	0.47	Ser	TCG	147-165	0.63-0.65
Gin	CAA	512-570	1.49-1.51	Ser	TCA	253-290	1.09-1.14
Gin	CAG	177-185	0.49-0.51	Ser	TCC	230-243	0.95-0.99
Glu	GAA	714-815	1.49-1.51	Thr	ACC	182-198	0.74
Glu	GAG	246-265	0.49-0.51	Thr	ACA	285-320	1.16-1.2
Gly	GGT	469-485	1.34-1.35	Thr	ACG	104-114	0.42-0.43
Gly	GGG	245-253	0.70	Thr	ACT	409-439	1.64-1.67
Gly	GGA	518-542	1.49-1.5	Trp	TGG	339-370	1.00
Gly	GGC	160-168	0.46	Tyr	TAC	139-159	0.39-0.4
His	CAT	353-380	1.51	Tyr	TAT	566-636	1.6-1.61
His	CAC	115-123	0.49	Val	GTA	398-418	1.46
Ile	ATC	298-327	0.56-0.57	Val	GTC	125-134	0.46-0.47
Ile	ATA	506-571	0.96-0.98	Val	GTG	159-167	0.58
Ile	ATT	773-850	1.46-1.47	Val	GTT	409-430	1.50
Leu	TTG	406-435	1.2-1.23	Ter	TAG	12-12	0.69-0.71
Leu	TTA	646-708	1.95-1.97	Ter	TGA	10-11	0.59-0.63
Leu	CTA	269-290	0.8-0.81	Ter	TAA	29-29	1.67-1.71

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不同产地珊瑚菜叶绿体基因组特征的差异性研究

Comparative Analysis of Glehnia littoralis from Different Geographic Regions Based on the Characteristics of Chloroplast Genome

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