The Evolutionary Relationship of Chromosomes in Seven Solanaceae Species

doi:10.16420/j.issn.0513-353x.2022-0328

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (5): 1009-1024.doi: 10.16420/j.issn.0513-353x.2022-0328

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

The Evolutionary Relationship of Chromosomes in Seven Solanaceae Species

FU Yu¹^,²^,^*, ZHANG Lingkui²^,^*, HUANG Yile², YANG Yinqing², CHEN Shumin², ZHANG Kang², LI Liangjun¹^,^**(), CHENG Feng²^,^**

¹College of Horticulture and Plant Protection，Yangzhou University，Yangzhou 225000，China
²Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China

Received:2022-06-17 Revised:2023-01-11 Online:2023-05-25 Published:2023-05-31
Contact: LI Liangjun, CHENG Feng E-mail:ljli@yzu.edu.cn

Abstract

Abstract:

In order to trace the evolution of chromosomes of Solanaceae species，a systematic comparative genomic analysis was carried out on seven Solanaceae species. Using the genome of model plant tomato as a reference template，the collinear relationship among seven species of Solanaceae were comprehensively identified，and the genome fragment unit system of Solanaceae was established. Based on this system，the ancestral genome of Solanaceae with 12 chromosomes was reconstructed. The results showed that the ancestral genome gradually formed the current genome structure of Solanaceae mainly through translocation and inversion of genome fragments，and these rearrangement events mostly occurred in the regions of centromere and other repeated sequences were enriched. This study provided an important theoretical reference for further understanding the genome evolution and species differentiation of Solanaceae and other plants.

Key words: Solanaceae, comparative genome, ancestral genome, chromosome rearrangement, centromere, repeat sequence

CLC Number:

S641

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.

Figures/Tables 7

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

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）.

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）.

Fig. 4 The inference process of Solanaceae ancestral chromosomes（A）and the rearrangement track of Solanaceae ancestral chromosomes in modern chromosomes（B）

Fig. 3 Examples of inference rules for ancestral chromosome connectivity relationship

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.

Fig. 6 Distribution of SlMBP3 in various species of Solanaceae

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The Evolutionary Relationship of Chromosomes in Seven Solanaceae Species

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