重要林木樟科植物全基因组测序研究进展

doi:10.11983/CBB23035

植物学报 ›› 2024, Vol. 59 ›› Issue (2): 302-318.DOI: 10.11983/CBB23035

重要林木樟科植物全基因组测序研究进展

杨智¹^,²^,³, 杨永¹^,²^,³^,^*()

¹南京林业大学南方现代林业协同创新中心, 南京 210037
²南京林业大学生物与环境学院, 南京 210037
³南京林业大学国家林业和草原局亚热带森林生物多样性保护重点实验室, 南京 210037

收稿日期:2023-03-13 接受日期:2023-11-14 出版日期:2024-03-01 发布日期:2023-12-04
通讯作者: * 杨永, 南京林业大学教授, 世界自然保护联盟(IUCN)物种生存委员会松柏类专家组主席, 博士生导师。长期从事植物分类、生物地理和濒危物种保护研究。发表论文(著) 150余篇(部), 主持国家自然科学基金和江苏省自然科学基金等项目。主编《世界裸子植物的分类和地理分布》获第十五届“上海图书奖”一等奖。目前其研究团队以裸子植物和樟科为研究对象, 开展整合分类学、生物地理和生物多样性保护等方面研究。E-mail: yongyang@njfu.edu.cn
基金资助:
国家重点研发计划(2022YFD2200100);国家自然科学基金(32270217);国家自然科学基金(31970205);江苏省自然科学基金(BK20211279);江苏省研究生科研创新计划(KYCX231117);南京林业大学水杉英才项目

Research Advances on Nuclear Genomes of Economically Important Trees of Lauraceae

Zhi Yang¹^,²^,³, Yong Yang¹^,²^,³^,^*()

¹Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
²College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
³Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China

Received:2023-03-13 Accepted:2023-11-14 Online:2024-03-01 Published:2023-12-04
Contact: * E-mail: yongyang@njfu.edu.cn

1. 附录.pdf(426KB)

摘要/Abstract

摘要： 近年来, 随着测序技术的革新、测序成本的降低和生物信息学软件的开发, 植物全基因组研究蓬勃发展。樟科(Lauraceae)隶属被子植物木兰类, 泛热带分布, 物种多样性高, 其中很多物种具有重要的经济和生态价值, 目前已发表包括8个物种的13个基因组。该文从樟科全基因组研究现状、基因组特征、起源和进化以及功能基因和基因家族4个方面进行综述, 着重介绍基于组学数据的木兰类及樟科的系统发生、樟科经历的多倍化事件以及与樟科花器官进化和代谢产物相关的基因鉴定。结合研究现状展望了樟科基因组研究的发展方向, 建议通过增加测序基因组分支的代表性并关注具有特殊价值的物种, 及研究物种特异性功能基因以加深对该家族基因功能和进化的理解。

关键词: 樟科, 演化, 核基因组, 功能基因, 系统发生

Abstract: With the rapid development of sequencing technology and bioinformatic analysis tools, the studies of plant genomes has been growing in an unprecedent speed. The family Lauraceae belongs to Magnoliids and is mainly found in pantropics with high species diversity. Species of this family are mostly woody and economically and ecologically important. Up to now, 13 genomes belonging to 8 species in the family Lauraceae have been published. Here, we review the recent advances on the published nuclear genomes of Lauraceae by focusing on their characteristics, evolution and phylogeny, and the functional genes and gene families. We highlight the recent achievements in the whole genome duplication events, and the genes/gene families related to the floral organ determination and metabolites in Lauraceae. Finally, we suggest further studies should be performed to improve our understanding of the function and evolution of this family by sequencing more species as well as more representative samples in all major clades, especially by tackling species with special value, and studying the species-specific functional genes.

Key words: Lauraceae, evolution, nuclear genome, function gene, phylogeny

杨智, 杨永. 重要林木樟科植物全基因组测序研究进展. 植物学报, 2024, 59(2): 302-318.

Zhi Yang, Yong Yang. Research Advances on Nuclear Genomes of Economically Important Trees of Lauraceae. Chinese Bulletin of Botany, 2024, 59(2): 302-318.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB23035

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图/表 7

图1 已测序乔木物种概况 (A) 已测序物种的生活型分布, 图中依次标注生活型、数量和占已测序维管植物数量的百分比(附录1); (B) 乔木数量最多的5个科测序情况。已测序物种数据来自Sun等(2022b); 生活型数据来自GIFT数据库(Weigelt et al., 2020)

Figure 1 Overview of sequenced tree species (A) The distribution of the growth form of sequenced species, growth form, species number and the percentage of the number of sequenced vascular plants were indicated (Appendix 1); (B) Overview of sequenced top five families with the largest number of tree species. The datasets of sequenced species were obtained from the paper of Sun et al. (2022b); the corresponding datasets of growth form were obtained from the GIFT database (Weigelt et al., 2020)

图2 樟科基因组已测序物种概况 (A) 樟科系统发生树(参考Liu et al., 2021); (B) 樟科物种已测序基因组数量折线图和各族测序物种基因组数量的饼图; (C) 近几年发表樟科基因组文章数量

Figure 2 Overview of sequenced species of Lauraceae (A) Phylogenetic tree of Lauraceae (refer to Liu et al., 2021); (B) Line chart of the number of sequenced genome of Lauraceae, and pie charts of numbers of sequenced species of every tribe; (C) Number of articles on Lauraceae genome in recent years

表1 已测序樟科基因组信息

Table 1 Information of sequenced Lauraceae genomes

序号	物种	族	基因组大小 (Mb)	染色体数目 (2n)	杂合度 (%)	编码基因数量	染色体挂载率 (%)	组装完整度 (BUSCO) (%)	注释完整度(BUSCO) (%)	测序方法	组装水平	参考文献
1	山苍子(Litsea cubeba)	月桂族(Laureae)	1325.7	24	-	31329	94.6	88.4	89.2	PacBio CLR和Hi-C	染色体	Chen et al., 2020b
2	朝鲜木姜子 (L. coreana)		1139.5	24	1.1	32445	97.1	94.0	-	Illumina、PacBio CCS和Hi-C	染色体	Zhang et al., 2022
3	山胡椒(Lindera glauca)		2092.2	24	1.4	65145	94.4	94.2	92.3	Illumina、Nanopor和Hi-C	染色体	Xiong et al., 2022
4	牛樟(Cinnamomum kanehirae=Camphora kanahirae)	樟族(Cinnamomeae)	730.7	24	-	27899	-	89.0	-	Illumina、PacBio CLR、‘Chicago’和Hi-C	染色体	Chaw et al., 2019
5	樟(C. camphora=Ca. officinarum)		755.4	24	-	24883	92.4	96.2	-	PacBio CCS和Hi-C	染色体	Jiang et al., 2022
6			723.1	24	1.2	36411	97.9	95.2	90.0	Illumina、PacBio CCS和Hi-C	染色体	Wang et al., 2022
7			719.9	24	2.9	28789	99.9	95.3	89.8	Illumina、PacBio CCS和Hi-C	染色体	Sun et al., 2022b
8			785.0	24	-	29919	85.4	95.2	90.8	PacBio CCS和Hi-C	染色体	Shen et al., 2022
9	阴香(C. burmanni)		1177.6	24	0.7	41549	98.8	89.7	-	Illumina、PacBio CLR和Hi-C	染色体	Li et al., 2022
10	闽楠(Phoebe bournei)	鳄梨族(Perseeae)	989.2	24	1.5	28198	-	95.0	81.0	PacBio CLR	Scaffold	Chen et al., 2020a
11	闽楠(Phoebe bournei)		941.8	24	1.4	30096	99.2	92.1	91.7	PacBio CLR、BioNano和Hi-C	染色体	Han et al., 2022
12	鳄梨(Persea americana)		912.6	24	-	24616	46.2	85.0	-	PacBio CLR	染色体	Rendón-Anaya et al., 2019
13	鳄梨(Persea americana)		913.0	24	-	42769	98.8	98.9	96.6	Illumina和PacBio CCS	染色体	Nath et al., 2022

图3 樟科各属染色体数目变化概率为染色体数目在该属中出现的比例。数据来自染色体数目数据库(CCDB, version 1.66) (Rice et al., 2015)及Oginuma和Tobe (2006) (附录2)

Figure 3 Variation in chromosome number of various genera in Lauraceae Cirde sizes represent the percentage occurrence of chromosome numbers across genera. The data was extracted from chromosome counts database (CCDB, version 1.66) (Rice et al., 2015) and result from Oginuma and Tobe (2006) (Appendix 2)

图4 已测序樟科基因组特征比较 (A) 基因组大小; (B) 基因组杂合度; (C) 重复序列比例; (D) 长末端重复序列比例

Figure 4 Comparison of characters of sequenced Lauraceae genomes (A) Genome sizes; (B) Genomic heterozygosity; (C) Ratio of repeat sequences; (D) Ratio of long terminal repeat

图5 樟科已测序物种系统发生关系 (A) 樟科已测序物种系统发生树(参考Liu et al., 2021; Han et al., 2022) (灰色椭圆形代表樟科经历的全基因组重复事件); (B) 从樟科基因组文献中得到的木兰类、真双子叶植物和单子叶植物系统发生关系的2种拓扑结构。

Figure 5 Phylogenetic relationships of sequenced species of Lauraceae (A) Phylogenetic tree of sequenced species in Lauraceae (refer to Liu et al., 2021; Han et al., 2022) (The grey ovals represent predicted whole genome duplication events in Lauraceae); (B) Two topologies of the relationship of magnoliids, eudicots and monocots in the published papers based on the studies on Lauraceae genomes

图6 樟科基因组功能基因研究热点

Figure 6 Research hotpots of functional genes of the Lauraceae genomes

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重要林木樟科植物全基因组测序研究进展

Research Advances on Nuclear Genomes of Economically Important Trees of Lauraceae

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