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Solanaceae pan-genomes reveal extensive fractionation and functional innovation of duplicated genes

文献类型： 外文期刊

作者： Zhang, Lingkui 1 ; Liu, Yuanhang 1 ; Huang, Yile 1 ; Zhang, Yiyue 1 ; Fu, Yu 1 ; Xiao, Ya 1 ; Chen, Shumin 1 ; Zhang, Kang 1 ; Cheng, Feng 1 ;

作者机构： 1.Chinese Acad Agr Sci, State Key Lab Vegetable Biobreeding, Sino Dutch Joint Lab Hort Genom Inst Vegetables &, Key Lab Biol & Genet Improvement Hort Crops,Minist, Beijing 100081, Peoples R China

2.Henan Agr Univ, Coll Hort, Zhengzhou, Peoples R China

3.Yangzhou Univ, Coll Hort & Plant Protect, Yangzhou, Peoples R China

4.Xiangxi Acad Agr Sci, Biotechnol Res Ctr, Jishou 416000, Hunan, Peoples R China

关键词： tomato; pepper; pan-genome; database; fruit; solanaceae

期刊名称：PLANT COMMUNICATIONS （ 影响因子：11.6； 五年影响因子：11.8 ）

ISSN： 2590-3462

年卷期： 2025 年 6 卷 3 期

页码：

收录情况： SCI

摘要： The Solanaceae family contains many agriculturally important crops, including tomato, potato, pepper, and tobacco, as well as other species with potential for agricultural development, such as the orphan crops groundcherry, wolfberry, and pepino. Research progress varies greatly among these species, with model crops like tomato being far ahead. This disparity limits the broader agricultural application of other Solanaceae species. In this study, we constructed an interspecies pan-genome for the Solanaceae family and identified various gene retention patterns. Our findings reveal that the activity of specific transposable elements is closely associated with gene fractionation and transposition. The pan-genome was further resolved at the level of T subgenomes, which were generated by Solanaceae-specific paleohexaploidization (T event). We demonstrate substantial gene fractionation (loss) and divergence events following ancient duplications. For example, all class A and E flower model genes in Solanaceae originated from two tandemly duplicated genes, which expanded through the g and T events before fractionating into 10 genes in tomato, each acquiring distinct functions critical for fruit development. Based on these results, we developed the Solanaceae Pan-Genome Database (SolPGD, http://www. bioinformaticslab.cn/SolPGD), which integrates datasets from both inter- and intra-species pan-genomes of Solanaceae. These findings and resources will facilitate future studies of solanaceous species, including orphan crops.

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