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

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

Abstract

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

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.

Figures/Tables 9

References 40

1	屠鹏飞, 冷青松, 徐国钧, 等. 莱阳参的生药鉴定 [J]. 中药材, 1999, 22(4): 174-176.
	Tu PF, Leng QS, Xu GJ, et al. Pharmacognostical studies on Radix glehniae (Glehnia littoralis) [J]. J Chin Med Mater, 1999, 22(4): 174-176.
2	安莹, 张姗姗, 张云, 等. 北沙参化学成分、药理作用研究进展及质量标志物(Q-Marker)预测 [J]. 中草药, 2024, 55(2): 640-656.
	An Y, Zhang SS, Zhang Y, et al. Research progress on chemical constituents, pharmacological effects and quality marker prediction of Glehniae radix [J]. Chin Tradit Herb Drugs, 2024, 55(2): 640-656.
3	Li SY, Xu N, Fang QQ, et al. Glehnia littoralis Fr. schmidtex miq.: a systematic review on ethnopharmacology, chemical composition, pharmacology and quality control [J]. J Ethnopharmacol, 2023, 317: 116831.
4	Chen Y, Lei LJ, Bi YQ, et al. Quality control of glehniae Radix, the root of Glehnia littoralis Fr. Schmidt ex miq., along its value chains [J]. Front Pharmacol, 2021, 12: 729554.
5	李宝国, 李军, 欧阳兵. 不同产地北沙参的氨基酸检测分析 [J]. 山东中医药大学学报, 2013, 37(5): 444-445.
	Li BG, Li J, Ouyang B. Amino acid detection and analysis of radix glehniae from different sources [J]. J Shandong Univ Tradit Chin Med, 2013, 37(5): 444-445.
6	叶国华, 张钦德, 许一平, 等. 不同产地北沙参中重金属含量的测定 [J]. 中药新药与临床药理, 2013, 24(4): 407-410.
	Ye GH, Zhang QD, Xu YP, et al. Determination of heavy metals in Radix glehniae from different producing areas [J]. Tradit Chin Drug Res Clin Pharmacol, 2013, 24(4): 407-410.
7	郑旭光, 陈钟, 项峰, 等. 河北道地药材北沙参HPLC - PDA指纹图谱研究 [J]. 药物分析杂志, 2011, 31(9): 1683-1688.
	Zheng XG, Chen Z, Xiang F, et al. Study on HPLC-PDA fingerprints of Radix glehniae from Hebei Province [J]. Chin J Pharm Anal, 2011, 31(9): 1683-1688.
8	刘小芬, 赖冰, 宋秀碧, 等. HPLC法分析闽产北沙参3种香豆素含量 [J]. 中国中医药现代远程教育, 2020, 18(10): 107-110.
	Liu XF, Lai B, Song XB, et al. Content analysis of three coumarins in glehniae Radix from Fujian Province by HPLC [J]. Chin Med Mod Distance Educ China, 2020, 18(10): 107-110.
9	张晴. 不同种源北沙参表型特征、香豆素类化合物含量及IPT基因表达差异研究 [D]. 烟台: 烟台大学, 2023.
	Zhang Q. Differences in phenotypic identificarion、coumarin content and expression of key enzyme genes in Glehnia littoralis from different origins [D]. Yantai: Yantai University, 2023.
10	张敏, 杨洪晓. 滨海沙滩珊瑚菜种群的空间格局及其对岸垄的响应 [J]. 生态学杂志, 2015, 34(1): 47-52.
	Zhang M, Yang HX. Spatial patterns of Glehnia littoralis population on sandy seashore and their responses to artificial beach ridge [J]. Chin J Ecol, 2015, 34(1): 47-52.
11	刘小芬, 张明孝, 陈勇, 等. 福建省长江澳珊瑚菜样地调查与群落特征 [J]. 中国野生植物资源, 2017, 36(6): 57-64.
	Liu XF, Zhang MX, Chen Y, et al. Sample plot investigation and community characteristics of Glehnia littoralis in changjiang'ao bay, Fujian Province [J]. Chin Wild Plant Resour, 2017, 36(6): 57-64.
12	An C, Ye KZ, Jiang RF, et al. Cytological analysis of flower development, insights into suitable growth area and genomic background: implications for Glehnia littoralis conservation and sustainable utilization [J]. BMC Plant Biol, 2024, 24(1): 895.
13	陈梓媛, 华中一, 袁媛. 全球物种数量最多的叶绿体基因组数据库的建立及应用进展 [J]. 中国中药杂志, 2024, 49(23): 6257-6263.
	Chen ZY, Hua ZY, Yuan Y. Establishment and application of chloroplast genome database with the largest number of species in world [J]. China J Chin Mater Med, 2024, 49(23): 6257-6263.
14	韩建萍, 宋经元, 姚辉, 等. 中药材DNA条形码鉴定的基因序列比较 [J]. 中国中药杂志, 2012, 37(8): 1056-1061.
	Han JP, Song JY, Yao H, et al. Comparison of DNA barcoders in identifying medicinal materials [J]. China J Chin Mater Med, 2012, 37(8): 1056-1061.
15	Chen SL, Yin XM, Han JP, et al. DNA barcoding in herbal medicine: Retrospective and prospective [J]. J Pharm Anal, 2023, 13(5): 431-441.
16	Lee SC, Lee HO, Kim K, et al. The complete chloroplast genome sequence of the medicinal plant Glehnia littoralis F.Schmidt ex Miq. (Apiaceae) [J]. Mitochondrial DNA A Part A, 2016, 27(5): 3674-3675.
17	Zhou YF, Geng ML, Li MM. The complete chloroplast genome of Glehnia littoralis, an Endangered medicinal herb of Apiaceae family [J]. Mitochondrial DNA B Resour, 2018, 3(2): 1013-1014.
18	孙月琪, 李密密, 周义峰. 珊瑚菜叶绿体基因组密码子使用偏性分析 [J]. 植物资源与环境学报, 2023, 32(6): 1-10.
	Sun YQ, Li MM, Zhou YF. Analysis on Codon usage bias of chloroplast genome of Glehnia littoralis [J]. J Plant Resour Environ, 2023, 32(6): 1-10.
19	Li WW, Liu SL, Wang SM, et al. A single origin and high genetic diversity of cultivated medicinal herb Glehnia littoralis subsp. littoralis (Apiaceae) deciphered by SSR marker and phenotypic analysis [J]. PLoS One, 2024, 19(8): e0308369.
20	Li WW, Li B, Zhang P, et al. Potential biological mechanisms underlying the endangered status of Glehnia littoralis revealed by nrDNA ITS and RAPD analyses [J]. Biotechnol Biotechnol Equip, 2020, 34(1): 1243-1251.
21	Robbins EHJ, Kelly S. The evolutionary constraints on angiosperm chloroplast adaptation [J]. Genome Biol Evol, 2023, 15(6): evad101.
22	Daniell H, Lin CS, Yu M, et al. Chloroplast genomes: diversity, evolution, and applications in genetic engineering [J]. Genome Biol, 2016, 17(1): 134.
23	Jin JJ, Yu WB, Yang JB, et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes [J]. Genome Biol, 2020, 21(1): 241.
24	Tillich M, Lehwark P, Pellizzer T, et al. GeSeq - versatile and accurate annotation of organelle genomes [J]. Nucleic Acids Res, 2017, 45(W1): W6-W11.
25	Greiner S, Lehwark P, Bock R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes [J]. Nucleic Acids Res, 2019, 47(W1): W59-W64.
26	Huang LJ, Yu HX, Wang Z, et al. CPStools: a package for analyzing chloroplast genome sequences [J]. iMetaOmics, 2024, 1(2): e25.
27	Beier S, Thiel T, Münch T, et al. MISA-web: a web server for microsatellite prediction [J]. Bioinformatics, 2017, 33(16): 2583-2585.
28	兰朝辉, 田徐芳, 师玉华, 等. 五月艾Artemisia indica叶绿体基因组结构及系统发育分析 [J]. 中国中药杂志, 2022, 47(22): 6058-6065.
	Lan CH, Tian XF, Shi YH, et al. Chloroplast genome structure characteristics and phylogenetic analysis of Artemisia indica [J]. China J Chin Mater Med, 2022, 47(22): 6058-6065.
29	胡健鹏, 蒋露, 徐睿, 等. 安徽岳西野生茅苍术叶绿体全基因组测序及系统发育研究 [J]. 中国中药杂志, 2023, 48(1): 52-59.
	Hu JP, Jiang L, Xu R, et al. Complete chloroplast genome sequencing and phylogeny of wild Atractylodes lancea from Yuexi, Anhui province [J]. China J Chin Mater Med, 2023, 48(1): 52-59.
30	Li HE, Guo QQ, Xu L, et al. CPJSdraw: analysis and visualization of junction sites of chloroplast genomes [J]. PeerJ, 2023, 11: e15326.
31	Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability [J]. Mol Biol Evol, 2013, 30(4): 772-780.
32	Minh BQ, Schmidt HA, Chernomor O, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era [J]. Mol Biol Evol, 2020, 37(5): 1530-1534.
33	Ronquist F, Teslenko M, van der Mark P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space [J]. Syst Biol, 2012, 61(3): 539-542.
34	Plunkett GM, Downie SR. Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily apioideae [J]. Syst Bot, 2000, 25(4): 648.
35	Zhu AD, Guo WH, Gupta S, et al. Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates [J]. New Phytol, 2016, 209(4): 1747-1756.
36	国家药典委员会. 中华人民共和国药典-一部: 2020年版 [M]. 北京: 中国医药科技出版社, 2020: 103.
	Pharmacopoeia Commission of the People's Republic of China. Pharmacopoeia of the People's Republic of China - Volume I: 2020 Edition [M]. Beijing: China Medical Science Press, 2020: 103.
37	鲁兆莉, 覃海宁, 金效华, 等. 《国家重点保护野生植物名录》调整的必要性、原则和程序 [J]. 生物多样性, 2021, 29(12): 1577-1582.
	Lu ZL, Qin HN, Jin XH, et al. On the necessity, principle, and process of updating the List of National Key Protected Wild Plants [J]. Biodivers Sci, 2021, 29(12): 1577-1582.
38	Guo YY, Yang JX, Bai MZ, et al. The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions [J]. BMC Plant Biol, 2021, 21(1): 248.
39	Wei N, Pérez-Escobar OA, Musili PM, et al. Plastome evolution in the hyperdiverse genus Euphorbia (Euphorbiaceae) using phylogenomic and comparative analyses: large-scale expansion and contraction of the inverted repeat region [J]. Front Plant Sci, 2021, 12: 712064.
40	王爱兰, 王贵琳, 李维卫. 濒危物种珊瑚菜遗传多样性的ISSR分析 [J]. 西北植物学报, 2015, 35(8): 1541-1546.
	Wang AL, Wang GL, Li WW. Genetic diversity of Glehnia littoralis populations revealed by ISSR molecular markers [J]. Acta Bot Boreali Occidentalia Sin, 2015, 35(8): 1541-1546.

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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