基于保护基因组学揭示荷叶铁线蕨的濒危机制

doi:10.17520/biods.2021508

生物多样性 ›› 2022, Vol. 30 ›› Issue (7): 21508. DOI: 10.17520/biods.2021508

• 研究报告: 遗传多样性 • 上一篇下一篇

基于保护基因组学揭示荷叶铁线蕨的濒危机制

孙维悦¹^,², 舒江平²^,³, 顾钰峰¹^,⁴, 莫日根高娃⁴, 杜夏瑾², 刘保东¹^,^*(), 严岳鸿²^,^*()

1.哈尔滨师范大学植物生物学黑龙江省高校重点实验室, 哈尔滨 150025
2.深圳市兰科植物保护研究中心, 广东深圳 518114
3.中国科学院华南植物园, 广州 510650
4.中国科学院上海辰山植物科学研究中心, 上海 201602

收稿日期:2021-12-09 接受日期:2022-04-09 出版日期:2022-07-20 发布日期:2022-06-21
通讯作者: 刘保东,严岳鸿
作者简介:99bd@163.com
*E-mail: yhyan@sibs.ac.cn;
基金资助:
生态环境部生物多样性调查与评估项目(2019HJ2096001006)

Conservation genomics analysis revealed the endangered mechanism of Adiantum nelumboides

Weiyue Sun¹^,², Jiangping Shu²^,³, Yufeng Gu¹^,⁴, Morigengaowa⁴, Xiajin Du², Baodong Liu¹^,^*(), Yuehong Yan²^,^*()

1. Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin 150025
2. The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong 518114
3. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650
4. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602

Received:2021-12-09 Accepted:2022-04-09 Online:2022-07-20 Published:2022-06-21
Contact: Baodong Liu,Yuehong Yan

摘要/Abstract

摘要：

理解物种的濒危机制对生物多样性的科学保护至关重要。荷叶铁线蕨(Adiantum nelumboides)作为国家一级重点保护野生植物, 其遗传多样性状况和濒危机制一直存在较大争议。本文利用简化基因组测序技术(genotyping by sequencing, GBS)对来自6个居群的28个荷叶铁线蕨样本测序, 共获得29.6 Gb的数据, 并筛选得到9,423个高质量单核苷酸变异位点(SNP), 通过遗传多样性和居群遗传结构分析, 并结合不同气候情景下物种潜在分布区差异, 探讨了荷叶铁线蕨的濒危原因和科学保护策略。结果表明: (1)荷叶铁线蕨具有较低的遗传多样性(H_o= 0.138、H_e= 0.232、P_i= 0.373), 同时种群间具有较低的遗传分化(F_st= 0.0202)和基因流(N_m= 1.9613); (2)所有样本均来自2个遗传分组, 基因组大小为 5.01‒5.83 Gb, 且均为四倍体, GC含量约为 39%‒41%; (3)生态位模拟表明, 与现代气候相比, 在未来气候变化下荷叶铁线蕨的潜在分布区面积略有增加, 但高适生区面积减小。其主要适生区向北迁移, 影响其分布的主导因子为昼夜温差月均值和最冷季降水量。正是由于荷叶铁线蕨遗传多样性低, 不同种群间遗传分化较低, 再加上气候条件的变化, 其适生区狭窄, 导致其遗传多样性和种群数量急剧下降。因此, 自身更新能力低以及过度的人为活动干扰可能是导致其濒危的主要原因。建议加强对荷叶铁线蕨的就地保护; 通过生境恢复及自然回归等措施, 增加居群间的基因交流, 防止遗传资源丢失加剧。

关键词: 遗传结构, 物种分布模型, 主导气候因子, 遗传多样性, 简化基因组测序

Abstract

Aims: Understanding the mechanism that leads species to endangerment is crucial to the conservation of biodiversity. Adiantum nelumboides is a key wild plant that is protected at the national level, and its genetic diversity and endangerment mechanism are controversial.
Methods: A total of 28 A. nelumboides samples, from six populations, were used to obtain single-nucleotide variation sites (SNP) by the genotyping by sequencing (GBS) method. The genetic diversity and structure of the population were analyzed and combined with the change in the potential distribution area of species under different climate scenarios. Then the possible causes of endangerment and scientific protection strategies of A. nelumboides were discussed.
Results: The results showed that 29.6 Gb of data was obtained based on the GBS sequencing, and 9,423 high-quality SNP loci were screened. Adiantum nelumboides had low genetic diversity (H_o = 0.138, H_e = 0.232, P_i = 0.373), low genetic differentiation (F_st = 0.0202) and gene flow (N_m = 1.9613). The A. nelumboides samples are from two ancestral haplotypes, their genome size was 5.01‒5.83 Gb, they were tetraploid, and the GC content was about 39%‒41%. Under future climate change, the potential distribution area of A. nelumboides will increase slightly, in which the area of high fitness is lost. The primary areas that are suitable for the plant are distributed in Wanzhou, Chongqing and further north. The dominant factors affecting its distribution are monthly mean differences in diurnal temperatures and precipitation during the coldest season.
Conclusions: Due to the low genetic diversity, lack of gene exchange between different populations, and changes in climatic conditions, suitable growth areas for A. nelumboides become narrow, resulting in a sharp decline in species diversity and population size. Therefore, their low regeneration ability and excessive disturbance from human activities might be the main reasons for the endangered status of A. nelumboides. It was recommended to strengthen in situ conservation of A. nelumboides. Measures such as habitat restoration and natural regression must be discussed to increase gene exchange across populations. At the same time, a core germplasm of this species must be constructed to prevent the aggravation of genetic resource loss.

Key words: genetic structure, species distribution models, dominant climate factor, genetic diversity, genotyping- by-sequencing

孙维悦, 舒江平, 顾钰峰, 莫日根高娃, 杜夏瑾, 刘保东, 严岳鸿 (2022) 基于保护基因组学揭示荷叶铁线蕨的濒危机制. 生物多样性, 30, 21508. DOI: 10.17520/biods.2021508.

Weiyue Sun, Jiangping Shu, Yufeng Gu, Morigengaowa, Xiajin Du, Baodong Liu, Yuehong Yan (2022) Conservation genomics analysis revealed the endangered mechanism of Adiantum nelumboides. Biodiversity Science, 30, 21508. DOI: 10.17520/biods.2021508.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2021508

https://www.biodiversity-science.net/CN/Y2022/V30/I7/21508

图/表 8

表1 荷叶铁线蕨样品采集信息

Table 1 Sample details of Adiantum nelumboides

居群 Population	采样地点 Sampling localities	样本数量 Sample size	样本采集号 Voucher no.
石柱 SZ	重庆市石柱县西沱镇 Xituo Town, Shizhu County, Chongqing	10	YYH15105, YYH15106, YYH15107, YYH15108, YYH15109, YYH15110, YYH15111, YYH15112, YYH15113, YYH15116
南川 NC	重庆市南川区 Nanchuan District, Chongqing	3	YSR0101, YSR0201, YSR0204
新乡 XX	重庆市万州区新乡镇 Xinxiang Town, Wanzhou District, Chongqing	8	YYH15091, YYH15071, YYH15072, YYH15088, YYH15087, YYH15092, YYH15090, YYH15086
燕山 YS	重庆市万州区燕山乡 Yanshan Town, Wanzhou District, Chongqing	1	YYH15070
武陵 WL	重庆市万州区武陵镇 Wuling Town, Wanzhou District, Chongqing	5	YYH15117, YYH15118, YYH15119, YYH15120, YYH15121
忠县 ZX	重庆市忠县石宝镇 Shibao Town, Zhong County, Chongqing	1	YYH15114

表2 荷叶铁线蕨相对荧光强度

Table 2 Relative fluorescence intensity of Adiantum nelumboides

样品 Sample	倍性 Ploidy level	内参荧光强度 Relative fluorescence intensity	待测荧光强度 Mean	基因组大小 Genome size
YYH15105	4X	62.96	151.86	5.55
YYH15111	4X	60.30	140.32	5.35
YYH15112	4X	60.06	130.77	5.01
YYH15116	4X	67.82	171.92	5.83

表3 不同居群荷叶铁线蕨遗传多样性。样品信息同表1。

Table 3 Genetic diversity indices of different groups of Adiantum nelumboides. The sample information see Table 1.

居群名称 Population	观察杂合度 H_o	期望杂合度 H_e	核苷酸多样性 P_i	近交系数 F_is
石柱 SZ	0.206	0.214	0.316	0.172
南川 NC	0.211	0.287	0.683	0.27
新乡 XX	0.104	0.285	0.1166	0
燕山 YS	0.106	0.135	0.105	0
武陵 WL	0.198	0.187	0.54	0.117
忠县 ZX	0.218	0.286	0.48	0.303
平均值 Average	0.173	0.232	0.373	0.143

表4 荷叶铁线蕨居群间的遗传分化系数(Fst: 对角线下)与基因流(Nm: 对角线上), 样品信息同表1。

Table 4 Genetic differentiation coefficient (Fst: below the diagonal) and gene flow (Nm: above the diagonal). The sample information is shown in Table 1.

居群 Population	石柱 SZ	南川 NC	燕山 YS	忠县 ZX	武陵 WL	新乡 XX
石柱 SZ		1.108	1.957	2.023	2.486	2.157
南川 NC	0.0216		1.795	2.417	2.186	1.957
燕山 YS	0.0194	0.0312		1.864	2.167	2.035
忠县 ZX	0.0165	0.0216	0.0183		2.341	1.628
武陵 WL	0.0186	0.0298	0.0161	0.0176		1.439
新乡 XX	0.0154	0.0251	0.0148	0.0193	0.0169

图1 基于SNP的荷叶铁线蕨遗传结构分析。A: 当K = 2时每个个体的遗传成分分析结果和基于9,423个SNP的最大似然法建树结果示。每一个柱形代表1个样本, 每种颜色代表1个遗传簇; B: 最佳聚类结果的地理分布, 其中的饼状图代表每个居群的遗传簇; C: 主成分分析结果, 图中每个点代表1个样品。样品信息同表1。

Fig. 1 Analysis of population structure based on identified SNP. A, Results of the admixture proportions for each individual with K = 2 and maximum likelihood tree based on 9,423 SNPs. Each sample is represented by a histogram, which is partitioned into different colors. Each color represents a genetic cluster. Numbers in the nodes are the bootstrap values from 100 replicates; B, The distribution of best results in clusters by Structure. The pie chart represents the genetic cluster of each population; C, Results of the principal component analysis. Each sample is represented by a point. The sample information is shown in Table 1.

图2 荷叶铁线蕨有效群体大小变化分析。A: 位点频谱; B: Stairway Plot基于SFS的群体大小变化。粗线为中位数, 阴影部分为95%置信区间。LGM: 末次盛冰期; LGP: 末次冰期。

Fig. 2 Changes in population size of Adiantum nelumboides. A, Folded site frequency spectrum (SFS); B, Changes in population size inferred by Stairway plot using folded site frequency spectrum (SFS). Thick lines represent the median, and shaded areas represent the 95% confidence intervals. LGM, Last glacial maximum; LGP, Last glacial period.

图3 不同时期荷叶铁线蕨适宜性生境分布。A: 末次盛冰期气候情景; B: 末次间冰期气候情景; C: 现代(1970?2000)气候情景; D: 未来(2081?2100) RCP2.6气候情景。

Fig. 3 Distribution of suitable habitats for Adiantum nelumboides in different periods. A, Last glacial maximum climate scenarios; B, Last interglacial climate scenarios; C, Contemporary (1970?2000) climate scenarios; D, Future (2081?2100) RCP2.6 climate scenarios.

图4 植物遗传多样性与濒危程度分析。CR: 极危; EN: 濒危; VU: 易危; LC: 无危; NE: 未予评估。图中数据来源于附录4参考文献。

Fig. 4 Genetic diversity and endangered degree. CR, Critically Endangered; EN, Endangered; VU, Vulnerable; LC, Least Concern; NE, Not Evaluated. Data in the figure were from the references listed in Appendix 4.

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	[ 余顺慧, 冉谷, 蒋雪梅, 邓洪平, 周兴成 (2013) 三峡库区珍稀濒危植物荷叶铁线蕨群落伴生维管植物研究. 广东农业科学, 40, 145-147.]

基于保护基因组学揭示荷叶铁线蕨的濒危机制

Conservation genomics analysis revealed the endangered mechanism of Adiantum nelumboides

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