<br>水蒺藜的泛基因组揭示了同种异体多倍体化后的结构变异和不对称亚基因组分歧,Horticulture Research

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水蒺藜的泛基因组揭示了同种异体多倍体化后的结构变异和不对称亚基因组分歧
Horticulture Research ( IF 7.6 ) Pub Date : 2023-10-13 , DOI: 10.1093/hr/uhad203
Xinyi Zhang _{1,

2} , Yang Chen _{1,

2} , Lingyun Wang ₃ , Ye Yuan ₄ , Mingya Fang ₃ , Lin Shi ₃ , Ruisen Lu ₅ , Hans Peter Comes ₆ , Yazhen Ma ₂ , Yuanyuan Chen ₂ , Guizhou Huang ₇ , Yongfeng Zhou ₇ , Zhaisheng Zheng ₃ , Yingxiong Qiu ₂

Affiliation

水蒺藜（Trapa spp.，Lythraceae）是一种传统但目前未得到充分利用的非谷类作物。在这里，我们为异体四倍体 T. natans （4x， AABB）的两个二倍体祖细胞生成了染色体水平的基因组组装，即二倍体 T. natans （2x， AA）和 T. incisa （2x， BB）。结合 Trapa 的四个已发表的（亚）基因组，我们使用基于基因和基于图形的泛基因组方法以及泛基因组转座因子（TE）文库来开发 Trapa 基因组资源。泛基因组表现出很大的基因内容变异，可有可无和私有基因簇占据了六个（子）基因组中总簇集的很大一部分（51.95%）。存在-缺失变异（PAV）的基因分型鉴定了 40,453 个 PAVs，与 2,570 个 A 或 B 系特异性基因相关，其中 1,428 个差异表达，并在器官发育过程、有机物质代谢过程和对刺激的反应中富集。比较基因组分析表明，异体四倍体 T. natans 经历了不对称的亚基因组分化，其中 B 亚基因组比 A 亚基因组更显性。包括 PAV 、 TE 的不对称扩增、同源交换（HE）和同源表达分歧在内的多种因素共同影响了多倍体化后的基因组进化。总体而言，这项研究揭示了 Trapa 的基因组结构和进化，并促进了其功能基因组研究和育种计划。

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Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization

Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid T. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and T. incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40,453 PAVs associated with 2,570 genes specific to A- or B-lineages, of which 1,428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.

更新日期：2023-10-13

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