Chinese Bulletin of Botany ›› 2024, Vol. 59 ›› Issue (2): 302-318.DOI: 10.11983/CBB23035 cstr: 32102.14.CBB23035
• SPECIAL TOPICS • Previous Articles Next Articles
Zhi Yang1,2,3, Yong Yang1,2,3,*()
Received:
2023-03-13
Accepted:
2023-11-14
Online:
2024-03-10
Published:
2024-03-10
Contact:
* E-mail: Zhi Yang, Yong Yang. Research Advances on Nuclear Genomes of Economically Important Trees of Lauraceae[J]. Chinese Bulletin of Botany, 2024, 59(2): 302-318.
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)
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
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., |
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., | |
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., | |
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., |
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., | |
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., | ||
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., | ||
8 | 785.0 | 24 | - | 29919 | 85.4 | 95.2 | 90.8 | PacBio CCS和Hi-C | 染色体 | Shen et al., | ||
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., | |
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., |
11 | 941.8 | 24 | 1.4 | 30096 | 99.2 | 92.1 | 91.7 | PacBio CLR、BioNano和Hi-C | 染色体 | Han et al., | ||
12 | 鳄梨(Persea americana) | 912.6 | 24 | - | 24616 | 46.2 | 85.0 | - | PacBio CLR | 染色体 | Rendón-Anaya et al., | |
13 | 913.0 | 24 | - | 42769 | 98.8 | 98.9 | 96.6 | Illumina和PacBio CCS | 染色体 | Nath et al., |
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., |
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., | |
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., | |
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., |
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., | |
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., | ||
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., | ||
8 | 785.0 | 24 | - | 29919 | 85.4 | 95.2 | 90.8 | PacBio CCS和Hi-C | 染色体 | Shen et al., | ||
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., | |
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., |
11 | 941.8 | 24 | 1.4 | 30096 | 99.2 | 92.1 | 91.7 | PacBio CLR、BioNano和Hi-C | 染色体 | Han et al., | ||
12 | 鳄梨(Persea americana) | 912.6 | 24 | - | 24616 | 46.2 | 85.0 | - | PacBio CLR | 染色体 | Rendón-Anaya et al., | |
13 | 913.0 | 24 | - | 42769 | 98.8 | 98.9 | 96.6 | Illumina和PacBio CCS | 染色体 | Nath et al., |
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)
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
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
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