1. College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing 100083
2. Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201
3. University of Chinese Academy of Sciences, Beijing 100049

摘要：

全球生物多样性的急剧下降促使人们对生物多样性的保护日益重视。保护遗传学是濒危物种保护研究的重要手段, 它极大地促进了人们对保护生物学多个领域的认知。然而, 保护生物学的一些重大科学问题, 包括濒危植物的演化历史、濒危原因和过程以及适应性演化机制等仍有待进一步深入研究。近年来, 高通量测序技术和保护遗传学思想的交叉融合, 促进了保护基因组学的产生, 为深入探讨这些重要问题提供了新的方法和思路。本文简要综述了组学方法中的全基因组重测序方法在濒危植物保护研究中取得的一些重要进展, 以期推动我国濒危植物保护生物学的进一步发展。全基因组重测序作为目前保护基因组学方法中具有最高分辨力的一种方法, 在研究濒危植物系统发育和种群遗传结构、基因组多样性、种群演化历史、适应性演化和近交衰退等方面取得了一些重要进展, 这些研究确定了一些濒危物种的分类地位和种群保护单元, 揭示了它们的进化历史、濒危原因和过程, 阐明了部分适应性进化和近交衰退的遗传机制。由于重测序方法可以更加深入地窥探保护生物学的诸多问题, 随着测序技术进一步发展和费用的降低, 它必将成为保护生物学研究的主要技术手段。

Abstract

Background & Aims: Increasing attention is focused on global change and loss of biodiversity. Genetics is an important tool in the conservation of threatened species, which have greatly promoted our understanding of diverse areas in conservation biology. However, some key scientific issues in conservation biology, including evolutionary history, endangered mechanism, genetic basis of adaptive evolution and inbreeding depression, are remain to be understood. Spurred by technological advances in high-throughput sequencing, conservation genomics are developed by using of new genomic techniques to solve problems in conservation biology, providing new approaches to deep understanding of the key issues in conservation biology. This paper briefly summarizes the important research progress in the conservation genomics based on whole genome resequencing, aiming to promote the conservation biology of threatened plant in China.
Progress: Whole genome resequencing, being the highest genomic resolution among current methods in conservation genomics, has made many significant advancements, including classification of phylogenetic relationships between unresolved taxa, the reconstruction of population structure, genomic diversity, demographic history, adaptive evolution and inbreeding depression. Based on these advancements, conservation taxa and conservation units are identified, the evolutionary history and endangered causes of species are revealed and the genetic basis of adaptive evolution and inbreeding depression are partly revealed.
Prospect: As whole-genome resequencing provides deep insights into the key issues in conservation biology, with the improvements of even higher throughput and lower cost, whole-genome resequencing will be a routine task in conservation biology studies.

Key words: whole genome resequencing, conservation genomics, endangered plants, adaptive evolution, inbreeding depression

景昭阳, 程可光, 舒恒, 马永鹏, 刘平丽 (2023) 全基因组重测序方法在濒危植物保护中的应用. 生物多样性, 31, 22679. DOI: 10.17520/biods.2022679 .

Zhaoyang Jing, Keguang Cheng, Heng Shu, Yongpeng Ma, Pingli Liu (2023) Whole genome resequencing approach for conservation biology of endangered plants. Biodiversity Science, 31, 22679. DOI: 10.17520/biods.2022679 .

图1 全基因组从头测序的受威胁植物统计。(a)已经全基因组测序的受威胁植物饼图。括号中的数字分别表示已经全基因组测序的受威胁植物物种数量及其所占总测序植物物种数量的比例。(b)《世界自然保护联盟红皮书》和2021年发布的《国家重点保护野生植物名录》收录的受威胁植物所属科统计图。图中的数字表示物种的数量。 Fig. 1 The species statistics with de novo whole-genome sequencing. (a) Comparison of threatened plant species and other plant species with de novo whole-genome sequencing. Values in bracket indicate the number of threatened plant species with de novo whole genome sequencing and its proportion to the total plant species with de novo whole genome sequencing. (b) The distribution of species with de novo whole-genome sequencing included in IUCN Red List of Threatened Species and the List of National Key Protected Wild Plants (2021) in different family. Values indicate the number of species in each family.

图1 全基因组从头测序的受威胁植物统计。(a)已经全基因组测序的受威胁植物饼图。括号中的数字分别表示已经全基因组测序的受威胁植物物种数量及其所占总测序植物物种数量的比例。(b)《世界自然保护联盟红皮书》和2021年发布的《国家重点保护野生植物名录》收录的受威胁植物所属科统计图。图中的数字表示物种的数量。

Fig. 1 The species statistics with de novo whole-genome sequencing. (a) Comparison of threatened plant species and other plant species with de novo whole-genome sequencing. Values in bracket indicate the number of threatened plant species with de novo whole genome sequencing and its proportion to the total plant species with de novo whole genome sequencing. (b) The distribution of species with de novo whole-genome sequencing included in IUCN Red List of Threatened Species and the List of National Key Protected Wild Plants (2021) in different family. Values indicate the number of species in each family.

学名 Scientific name	濒危等级 Endangered category	保护等级 Protection level	θπ	样本量 Sample size	参考文献 References
野生稻 Oryza rufipogon	极危 CR	Ⅱ级 Class II	0.003000	446	Huang et al, 2012
天目铁木 Ostrya rehderiana	极危 CR	I级 Class I	0.001660	13	Yang et al, 2018
野生莲 Nelumbo nucifera	-	II级 Class II	0.002177	7	Huang et al, 2018
鹅掌楸 Liriodendron chinense	-	II级 Class II	0.001280	14	Chen et al, 2019
银杏 Ginkgo biloba	极危 CR	I级 Class I	0.002110	545	Zhao et al, 2019
水青树 Tetracentron sinense		II级 Class II	0.012800	55	Liu et al, 2020
细叶杨 Populus ilicifolia	易危 VU	-	0.000830	19	Chen Z et al, 2020
珙桐 Davidia involucrate	-	I级 Class I	0.005850	10	Chen Y et al, 2020
连香树 Cercidiphyllum japonicum	-	II级 Class II	0.001100	82	Zhu et al, 2020
小粒咖啡 Coffea arabica	濒危 EN	-	0.003810	48	Huang et al, 2020
朱红大杜鹃 Rhododendron griersonianum	极危 CR	-	0.001940	31	Ma et al, 2021a
胡桃 Juglans regia	易危 VU	II级 Class II	0.000500	55	Bernard et al, 2021
斧翅沙芥 Pugionium dolabratum	-	II级 Class II	0.013000	20	Hu et al, 2021
茶 Camellia sinensis	-	II级 Class II	0.006100	120	Lu et al, 2021
野生荔枝 Litchi chinensis	-	II级 Class II	0.008300	38	Hu et al, 2022
漾濞槭 Acer yangbiense	濒危 EN	-	0.003130	105	Ma et al, 2022
芒苞草 Acanthochlamys bracteata	易危 VU	-	0.000460	14	Xu et al, 2022
野大豆 Glycine soja	-	II级 Class II	0.001220	40	Wang et al, 2022

表1 受威胁植物核酸多样性

Table 1 Nucleic acid diversity of threatened plant species

学名 Scientific name	濒危等级 Endangered category	保护等级 Protection level	θπ	样本量 Sample size	参考文献 References
野生稻 Oryza rufipogon	极危 CR	Ⅱ级 Class II	0.003000	446	Huang et al, 2012
天目铁木 Ostrya rehderiana	极危 CR	I级 Class I	0.001660	13	Yang et al, 2018
野生莲 Nelumbo nucifera	-	II级 Class II	0.002177	7	Huang et al, 2018
鹅掌楸 Liriodendron chinense	-	II级 Class II	0.001280	14	Chen et al, 2019
银杏 Ginkgo biloba	极危 CR	I级 Class I	0.002110	545	Zhao et al, 2019
水青树 Tetracentron sinense		II级 Class II	0.012800	55	Liu et al, 2020
细叶杨 Populus ilicifolia	易危 VU	-	0.000830	19	Chen Z et al, 2020
珙桐 Davidia involucrate	-	I级 Class I	0.005850	10	Chen Y et al, 2020
连香树 Cercidiphyllum japonicum	-	II级 Class II	0.001100	82	Zhu et al, 2020
小粒咖啡 Coffea arabica	濒危 EN	-	0.003810	48	Huang et al, 2020
朱红大杜鹃 Rhododendron griersonianum	极危 CR	-	0.001940	31	Ma et al, 2021a
胡桃 Juglans regia	易危 VU	II级 Class II	0.000500	55	Bernard et al, 2021
斧翅沙芥 Pugionium dolabratum	-	II级 Class II	0.013000	20	Hu et al, 2021
茶 Camellia sinensis	-	II级 Class II	0.006100	120	Lu et al, 2021
野生荔枝 Litchi chinensis	-	II级 Class II	0.008300	38	Hu et al, 2022
漾濞槭 Acer yangbiense	濒危 EN	-	0.003130	105	Ma et al, 2022
芒苞草 Acanthochlamys bracteata	易危 VU	-	0.000460	14	Xu et al, 2022
野大豆 Glycine soja	-	II级 Class II	0.001220	40	Wang et al, 2022

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