园艺学报 ›› 2023, Vol. 50 ›› Issue (5): 1009-1024.doi: 10.16420/j.issn.0513-353x.2022-0328
付钰1,2,*, 张令奎2,*, 黄议乐2, 杨印庆2, 陈姝敏2, 张亢2, 李良俊1,**(), 程锋2,**
收稿日期:
2022-06-17
修回日期:
2023-01-11
出版日期:
2023-05-25
发布日期:
2023-05-31
通讯作者:
**(E-mail:ljli@yzu.edu.cn)(E-mail:chengfeng@caas.cn)作者简介:
*共同第一作者
基金资助:
FU Yu1,2,*, ZHANG Lingkui2,*, HUANG Yile2, YANG Yinqing2, CHEN Shumin2, ZHANG Kang2, LI Liangjun1,**(), CHENG Feng2,**
Received:
2022-06-17
Revised:
2023-01-11
Published:
2023-05-25
Online:
2023-05-31
摘要:
为了追溯茄科(Solanaceae)物种染色体的演化关系,对7种茄科物种进行了系统的比较基因组学分析,利用模式植物番茄的基因组为参考模板,全面鉴定7个物种间的基因组共线性关系,以此为基础建立了茄科的基因组片段单元系统,并基于该系统重建了具有12条染色体的祖先基因组,阐明祖先基因组主要通过基因组片段的易位和倒位逐步形成目前的茄科基因组结构,且这些重排事件多发生在着丝粒等重复序列富集的区域。研究结果为深入认识茄科以及其他植物的基因组进化和物种分化等提供理论参考。
中图分类号:
付钰, 张令奎, 黄议乐, 杨印庆, 陈姝敏, 张亢, 李良俊, 程锋. 7种茄科植物染色体的演化关系研究[J]. 园艺学报, 2023, 50(5): 1009-1024.
FU Yu, ZHANG Lingkui, HUANG Yile, YANG Yinqing, CHEN Shumin, ZHANG Kang, LI Liangjun, CHENG Feng. The Evolutionary Relationship of Chromosomes in Seven Solanaceae Species[J]. Acta Horticulturae Sinica, 2023, 50(5): 1009-1024.
物种 Species | 染色体数 Chromosome number | 品种名/版本 Cultivar name/Version | 染色体上基因数 Gene number |
---|---|---|---|
番茄 Solanum lycopersicum | 12 | SL4.0 | 33 562 |
马铃薯 Solanum tuberosum | 12 | DM v6.1 | 32 819 |
茄子 Solanum melongena | 12 | V4.1 | 33 644 |
辣椒 Capsicum annuum | 12 | CM334 | 31 600 |
菇娘果 Physalis floridana | 12 | V1 | 31 878 |
枸杞 Lycium barbarum | 12 | V1 | 33 431 |
烟草 Nicotiana tabacum | 24 | NIATTr2 | 35 519 |
葡萄 Vitis vinifera | 19 | 12X | 26 588 |
咖啡 Coffea canephora | 11 | V1 | 25 574 |
表1 基因组信息
Table 1 Information of genomes
物种 Species | 染色体数 Chromosome number | 品种名/版本 Cultivar name/Version | 染色体上基因数 Gene number |
---|---|---|---|
番茄 Solanum lycopersicum | 12 | SL4.0 | 33 562 |
马铃薯 Solanum tuberosum | 12 | DM v6.1 | 32 819 |
茄子 Solanum melongena | 12 | V4.1 | 33 644 |
辣椒 Capsicum annuum | 12 | CM334 | 31 600 |
菇娘果 Physalis floridana | 12 | V1 | 31 878 |
枸杞 Lycium barbarum | 12 | V1 | 33 431 |
烟草 Nicotiana tabacum | 24 | NIATTr2 | 35 519 |
葡萄 Vitis vinifera | 19 | 12X | 26 588 |
咖啡 Coffea canephora | 11 | V1 | 25 574 |
图1 茄科物种基因组进化特征以及比较基因组分析 A:茄科植物与参照物种的系统发育树及基因家族扩张与收缩情况(红色星表示WGT-γ事件,绿色星表示WGT-T事件)及已测序的7个茄科植物基因组之间的共线性片段关系。B:茄科物种同源基因的Ks分布图。C:茄科基因之间共线性基因对统计信息(红色字表示共线性基因占红色框中基因组的比例,绿色字表示共线性基因占绿色框中基因组的比例)。
Fig. 1 Genome evolution characteristics and comparative genomic analysis of Solanaceae A:Phylogenetic tree and gene family expansion and contraction of Solanaceae and reference species(red star represents WGT-γ event,green star represents WGT-T event)and collinear fragment relationships among sequenced genomes of seven Solanaceae species. B:The Ks distributions of homologous gene of Solanaceae species. C:Statistical information on intragroup collinear gene pairs among Solanaceae genomes(red fonts represent the proportion of collinear genes in the genome of the red box,and green fonts represent the proportion of collinear genes in the genome of the green box).
图2 番茄基因组片段(GB)划分规则及分布 A:番茄与其他茄科植物的共线性基因点阵图。B:番茄基因组中27个GB(S1 ~ S27)的分布及着丝粒大体位置(每个GB的颜色由祖先基因组AN5的染色体决定,黑色圆圈表示着丝粒大致位置)。
Fig. 2 Genomic block division rules and distribution of tomato A:Collinear gene dot plot of tomato and other Solanaceae species. B:Distribution of 27 GBs(S1-S27)in tomato genome and general location of centromere(The color of each GB is determined by the chromosomes of the ancestral genome AN5. Black ellipse indicates the approximate location of the centromeres).
图4 茄科祖先染色体推断过程(A)和茄科祖先染色体在现代染色体的重排轨迹(B)
Fig. 4 The inference process of Solanaceae ancestral chromosomes(A)and the rearrangement track of Solanaceae ancestral chromosomes in modern chromosomes(B)
图5 茄科基因组中重组染色体的区域特征(A)和保守染色体的区域特征(B) 图中染色体第3行为马铃薯着丝粒序列在茄科物种中最佳匹配序列密度图,黑色圆圈表示着丝粒候选位置。GD:基因密度;BM:最佳匹配度;RD:重复序列密度。
Fig. 5 Regional characteristics of chromosomal rearrangement in Solanaceae(A)and reginal characteristics of recombinant chromosomes in Solanaceae genome(B) The third row of chromosomes in the figure shows the density of the best matching sequence of potato centromere sequences in Solanaceae species. Black ellipse indicates approximate centromere location. GD:Gene density;BM:Best match;RD:Repeat density.
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