基于叶绿体基因组的江南牡丹草遗传多样性与遗传结构

doi:10.17520/biods.2025149

生物多样性 ›› 2025, Vol. 33 ›› Issue (8): 25149. DOI: 10.17520/biods.2025149 cstr: 32101.14.biods.2025149

• 遗传多样性及保护专题 • 上一篇下一篇

基于叶绿体基因组的江南牡丹草遗传多样性与遗传结构

李慧霞¹^,², 李玉¹, 宁馨¹, 李晓晨¹, 王天瑞¹, 宋以刚¹, 戴锡玲², 郑斯斯¹^,^*(), 钟鑫¹^,^*()

¹ 上海辰山植物园华东野生濒危资源植物保育中心, 上海 201602
² 上海师范大学生命科学学院, 上海 200234

收稿日期:2025-04-27 接受日期:2025-08-12 出版日期:2025-08-20 发布日期:2025-09-30
通讯作者: *共同通讯作者E-mail: zhengsisi1228@163.com;zhongxin@csnbgsh.cn
基金资助:
上海市绿化和市容管理局科研专项(G22204);上海市绿化和市容管理局科研专项(G242415)

Genetic diversity and genetic structure of Gymnospermium kiangnanense based on chloroplast genome

Huixia Li¹^,², Yu Li¹, Xin Ning¹, Xiaochen Li¹, Tianrui Wang¹, Yigang Song¹, Xiling Dai², Sisi Zheng¹^,^*(), Xin Zhong¹^,^*()

¹ Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
² College of Life Sciences, Shanghai Normal University, Shanghai 200234, China

Received:2025-04-27 Accepted:2025-08-12 Online:2025-08-20 Published:2025-09-30
Contact: *Co-authors for correspondence. E-mail: zhengsisi1228@163.com;zhongxin@csnbgsh.cn
Supported by:
Scientific Research of Shanghai Landscaping and City Appearance Administrative Bureau(G22204);Scientific Research of Shanghai Landscaping and City Appearance Administrative Bureau(G242415)

1. 附录.pdf(8248KB)

摘要/Abstract

摘要：

江南牡丹草(Gymnospermium kiangnanense)是分布于安徽和浙江的中国特有濒危植物, 已被纳入当地的珍稀濒危植物名录, 然而对其种群间遗传结构的相关研究较少。为了加强对江南牡丹草的保护, 本研究通过组装6个种群39个个体的叶绿体基因组序列并对其进行比较基因组学分析和种群遗传结构分析, 探讨了对江南牡丹草的保护策略。结果表明: (1)江南牡丹草叶绿体基因组在序列组成、基因结构和基因含量等方面都高度保守, 其中简单重复序列(simple sequence repeats, SSRs)类型表现出明显的种群特征; (2)叶绿体基因组中3个非编码区域: psbZ与trnG-GCC的间隔区(psbZ-trnG-GCC)、trnT-UGU与trnL-UAA的间隔区(trnT-UGU-trnL-UAA)以及ycf1与ndhF的间隔区(ycf1-ndhF), 均表现出较高的变异性, 同时ndhF具有较高的核苷酸多样性, 可作为潜在的分子标记; (3)叶绿体基因组具有较高的遗传多样性, 且种群间具有较高的遗传分化; (4) 6个种群39个个体的叶绿体基因组序列计算得出14个单倍型, 经过Network分析和Beast分析可以划分为3个支系; (5)江南牡丹草种群间的变异大, 且具有明显的谱系地理结构; (6)通过种群历史动态分析发现, 江南牡丹草种群未发生扩张, 一直处于平衡状态。江南牡丹草以异交的繁殖方式增加遗传变异、减少近交衰退, 再加上在中国东部存在的第四纪冰期避难所为其提供了稳定的生存环境, 因而其种群的遗传多样性较高。结实率低、种子扩散能力弱以及过度的人为活动可能是导致其濒危的主要原因, 因此通过对江南牡丹草叶绿体基因组的分析结合保护遗传学提出如下保护建议: (1)按支系划分3个保护单元, 重点保护浙江诸暨凤林下村种群, 设立保护小区; (2)在其花期进行人工放蜂, 增加传粉率和结实率; (3)降低群落的种群密度以改善光照, 促进幼苗生长; (4)在就地保护基础上, 于适宜植物园开展迁地保护与人工繁育; (5)加强科普宣传, 减少人为破坏; (6)合理利用其药用价值, 促进人工繁育与保护。

关键词: 江南牡丹草, 叶绿体基因组, 比较基因组学, 种群遗传结构

Abstract

Aims: Gymnospermium kiangnanense is a rare and endangered plant species endemic to China. Its distribution is restricted to Anhui and Zhejiang provinces, and it has been catalogued in the local registry of rare and endangered flora. However, there is relatively little research on it. Therefore, to investigate the genetic structure and elucidate the endangered mechanisms of G. kianganese, we conducted a comprehensive analysis based on its chloroplast genome, leading to evidence-based conservation recommendations.

Methods: This study assembled chloroplast genome sequences from 39 individuals across 6 populations to enhance the conservation of G. kiangnanense. Based on these chloroplast genomes, comparative genomic analyses and population genetic structure analyses were conducted to explore conservation strategies for G. kiangnanense.

Results: (1) The chloroplast genome of G. kiangnanense was highly conserved in terms of sequence composition, gene structure, and gene content, among which simple sequence repeats (SSRs) types exhibited obvious population characteristics. (2) The three non-coding regions in the chloroplast genome, namely spacer between psbZ and trnG-GCC (psbZ-trnG-GCC), spacer between trnT-UGU and trnL-UAA (trnT-UGU-trnL-UAA), and spacer between ycf1 and ndhF (ycf1-ndhF), all exhibited high variability. Meanwhile, the ndhF gene also showed high nucleotide diversity, suggesting that these regions had potential as molecular markers. (3) The chloroplast genome showed high genetic diversity and high genetic differentiation among populations. (4) Analysis of 39 chloroplast genome sequences from 6 populations identified 14 haplotypes, which were classified into 3 distinct lineages through Network and Beast analyses. (5) The variation among the populations of G. kiangnanense was significant, and it had a clear geographical structure of lineages. (6) Demographic history analysis indicated a stable population size in G. kiangnanense, with no evidence of past expansion.

Conclusion: Gymnospermium kiangnanense employs an outcrossing reproductive strategy, which not only enhances genetic variation but also mitigates inbreeding depression. Moreover, the existence of glacial refugia in eastern China during the Quaternary Ice Age offered a stable habitat for this species, thereby further promoting its population genetic diversity. Nevertheless, several factors are likely contributing to its endangered status, including low seed-setting rates, limited seed dispersal capacity, and excessive human activities. Therefore, based on the analysis of the chloroplast genome and conservation genetics of G. kiangnanense, the following conservation strategies are proposed: (1) Establish three conservation units according to distinct genetic lineages, with priority given to protecting the Fenglinxia Village population in Zhuji, Zhejiang Province, through the creation of a conservation area. (2) Implement managed bee pollination during the flowering period to enhance pollination and seed set rates. (3) Reduce population density to improve light availability for seedlings and promote their growth. (4) Complement in situ conservation with ex situ efforts by establishing artificial breeding programs in suitable botanical gardens. (5) Strengthen scientific outreach to minimize anthropogenic disturbances. (6) Promote its propagation and conservation through rational exploitation of its medicinal value in pharmaceutical development.

Key words: Gymnospermium kiangnanense, chloroplast genome, comparative genomics, population genetic structure

李慧霞, 李玉, 宁馨, 李晓晨, 王天瑞, 宋以刚, 戴锡玲, 郑斯斯, 钟鑫 (2025) 基于叶绿体基因组的江南牡丹草遗传多样性与遗传结构. 生物多样性, 33, 25149. DOI: 10.17520/biods.2025149.

Huixia Li, Yu Li, Xin Ning, Xiaochen Li, Tianrui Wang, Yigang Song, Xiling Dai, Sisi Zheng, Xin Zhong (2025) Genetic diversity and genetic structure of Gymnospermium kiangnanense based on chloroplast genome. Biodiversity Science, 33, 25149. DOI: 10.17520/biods.2025149.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2025149

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图/表 8

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采集地 Locality	种群代码 Population code	经度 Longitude	纬度 Latitude	海拔 Altitude (m)	个体数量 Number of individuals	单倍型(个体数) Haplotype (number of individuals)	h	π
安徽池州贵池石门村 Shimen Village, Guichi, Chizhou, Anhui	AGS	117.75° E	30.33° N	253.67	4	H1 (3), H2 (1)	0.50	0.003
浙江杭州淳安菖蒲村 Changpu Village, Chun’an, Hangzhou, Zhejiang	ZCC	119.13° E	29.95° N	124.00	8	H3 (8)	0	0
浙江杭州西湖仙桥洞 Xianqiao Cave, West Lake, Hangzhou, Zhejiang	ZHL	120.03° E	30.11° N	708.24	8	H4 (8)	0	0
浙江临安河桥陆平下村 Lupingxia Village, Heqiao, Lin’an, Zhejiang	ZLH	119.27° E	30.11° N	557.88	3	H5 (1), H6 (2)	0.67	0.0026
浙江诸暨半丘村 Banqiu Village, Zhuji, Zhejiang	ZZB	120.29° E	29.45° N	524.58	8	H7 (3), H8 (1), H9 (4)	0.68	0.0023
浙江诸暨凤林下村 Fenglinxia Village, Zhuji, Zhejiang	ZZF	120.25° E	29.51° N	155.47	8	H10 (1), H11 (2), H12 (2), H13 (1), H14 (2)	0.89	0.0049

采集地 Locality	种群代码 Population code	经度 Longitude	纬度 Latitude	海拔 Altitude (m)	个体数量 Number of individuals	单倍型(个体数) Haplotype (number of individuals)	h	π
安徽池州贵池石门村 Shimen Village, Guichi, Chizhou, Anhui	AGS	117.75° E	30.33° N	253.67	4	H1 (3), H2 (1)	0.50	0.003
浙江杭州淳安菖蒲村 Changpu Village, Chun’an, Hangzhou, Zhejiang	ZCC	119.13° E	29.95° N	124.00	8	H3 (8)	0	0
浙江杭州西湖仙桥洞 Xianqiao Cave, West Lake, Hangzhou, Zhejiang	ZHL	120.03° E	30.11° N	708.24	8	H4 (8)	0	0
浙江临安河桥陆平下村 Lupingxia Village, Heqiao, Lin’an, Zhejiang	ZLH	119.27° E	30.11° N	557.88	3	H5 (1), H6 (2)	0.67	0.0026
浙江诸暨半丘村 Banqiu Village, Zhuji, Zhejiang	ZZB	120.29° E	29.45° N	524.58	8	H7 (3), H8 (1), H9 (4)	0.68	0.0023
浙江诸暨凤林下村 Fenglinxia Village, Zhuji, Zhejiang	ZZF	120.25° E	29.51° N	155.47	8	H10 (1), H11 (2), H12 (2), H13 (1), H14 (2)	0.89	0.0049

基因分类 Genetic classification	基因分组 Group of gene	基因名称 Name of genes
光合作用相关基因 Photosynthesis-related genes	光合系统I Photosystem I	psaA, psaB, psaC, psaI, psaJ
	光合系统II Photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	NADH脱氢酶 NADPH dehydrogenase	ndhA^, ndhB^(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
	细胞色素b/f蛋白复合体 Cytochrome b/f protein complex	petA, petB^, petD^, petG, petL, petN
	ATP合酶 ATP synthase	atpA, atpB, atpE, atpF^, atpH, atpI*
	核糖体大亚基 Large ribosomal subunit	rbcL
转录翻译相关基因 Transcription- and translation-related genes	核糖体大亚基蛋白质 Large ribosomal subunit proteins	rpl14, rpl16^, rpl2^(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36
	核糖体小亚基蛋白质 Small ribosomal subunit proteins	rps11, rps12^*(2), rps14, rps15, rps16^, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8
	RNA聚合酶亚基 RNA polymerase subunit	rpoA, rpoB, rpoC1^, rpoC*2
	核糖体RNA Ribosomal RNA	rrn16(2), rrn23(2), rrn4.5(2), rrn5(2)
	转运RNA Transfer RNA	trnA-UGC^(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC^, trnH-GUG, trnI-CAU(2), trnI-GAU^(2), trnK-UUU^, trnL-CAA(2), trnL-UAA^, trnL-UAG, trnM-CAU, trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2), trnV-UAC^, trnW-CCA, trnY-GUA, trnfM-CAU
物质合成相关基因 Biosynthesis-related genes	成熟酶 Maturase	matK
	蛋白酶 Protease	clpP^**
	包裹膜蛋白 Envelop membrane protein	cemA
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD
	c型细胞色素合成基因 c-type cytochrome synthesis gene	ccsA
	转录起始因子 Transcription initiation factors	infA
未知功能基因 Uncharacterized genes	保守的叶绿体假设开放阅读框 Conserved hypothetical chloroplast open reading frames	ycf1(2), ycf2(2), ycf3^*, ycf*4

基因分类 Genetic classification	基因分组 Group of gene	基因名称 Name of genes
光合作用相关基因 Photosynthesis-related genes	光合系统I Photosystem I	psaA, psaB, psaC, psaI, psaJ
	光合系统II Photosystem II	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	NADH脱氢酶 NADPH dehydrogenase	ndhA^, ndhB^(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
	细胞色素b/f蛋白复合体 Cytochrome b/f protein complex	petA, petB^, petD^, petG, petL, petN
	ATP合酶 ATP synthase	atpA, atpB, atpE, atpF^, atpH, atpI*
	核糖体大亚基 Large ribosomal subunit	rbcL
转录翻译相关基因 Transcription- and translation-related genes	核糖体大亚基蛋白质 Large ribosomal subunit proteins	rpl14, rpl16^, rpl2^(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36
	核糖体小亚基蛋白质 Small ribosomal subunit proteins	rps11, rps12^*(2), rps14, rps15, rps16^, rps18, rps19, rps2, rps3, rps4, rps7(2), rps8
	RNA聚合酶亚基 RNA polymerase subunit	rpoA, rpoB, rpoC1^, rpoC*2
	核糖体RNA Ribosomal RNA	rrn16(2), rrn23(2), rrn4.5(2), rrn5(2)
	转运RNA Transfer RNA	trnA-UGC^(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC^, trnH-GUG, trnI-CAU(2), trnI-GAU^(2), trnK-UUU^, trnL-CAA(2), trnL-UAA^, trnL-UAG, trnM-CAU, trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2), trnV-UAC^, trnW-CCA, trnY-GUA, trnfM-CAU
物质合成相关基因 Biosynthesis-related genes	成熟酶 Maturase	matK
	蛋白酶 Protease	clpP^**
	包裹膜蛋白 Envelop membrane protein	cemA
	乙酰辅酶A羧化酶 Acetyl-CoA carboxylase	accD
	c型细胞色素合成基因 c-type cytochrome synthesis gene	ccsA
	转录起始因子 Transcription initiation factors	infA
未知功能基因 Uncharacterized genes	保守的叶绿体假设开放阅读框 Conserved hypothetical chloroplast open reading frames	ycf1(2), ycf2(2), ycf3^*, ycf*4

变异来源 Source of variation	自由度 df	平方和 Sum of squares	变异成分 Variance components	变异率 Percentage of variation (%)
种群间 Among populations	5	2,430.279	76.38595	99.58
种群内 Within populations	33	10.542	0.31944	0.42
F_ST	0.99584

基于叶绿体基因组的江南牡丹草遗传多样性与遗传结构

Genetic diversity and genetic structure of Gymnospermium kiangnanense based on chloroplast genome

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