Wu Haolin, Yang Wenjie, Dong Guanyong, Hu Quanjun, Li Dawei, Liu Jianquan
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 1st Ring Road, Chengdu, 610065, China.
Department of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), No. 184 Xinqiao Street, Chongqing, 400037, China.
Hortic Res. 2025 Mar 3;12(6):uhaf067. doi: 10.1093/hr/uhaf067. eCollection 2025 Jun.
Kiwifruits, belonging to the genus , are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of , leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6 Mb. By compiling these haplotype genomes, we constructed a super pan-genome for the genus. We identified numerous structural variations (SVs, including variations in gene copy number) and highly diverged regions in these genomes. Notably, significant SV variability was observed within the intronic regions of the and genes across different materials, suggesting their potential roles in influencing fruit size and trichome formation. Intriguingly, our findings indicated a high genetic divergence between two haplotype genomes, with one individual, tentatively named , from sect. . This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker, particularly through the upregulation of the gene, which contains a specific SV, after infection by pv. . In addition, we also discussed the interlineage hybridizations and taxonomic treatments of the genus . Overall, the comprehensive pan-genome constructed here, along with our findings, lays a foundation for examining genetic compositions and markers, particularly those related to SVs, to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits.
猕猴桃属于猕猴桃属，被公认为是20世纪最成功驯化的水果之一。尽管该属拥有丰富的野生资源和多样的表型，但对其基因组变化的了解仍然有限。在这里，我们对来自猕猴桃属高度多样化组的7个代表性材料进行了全基因组测序，从而组装和注释了14个单倍型基因组，其大小范围为602.0至699.6 Mb。通过汇编这些单倍型基因组，我们构建了猕猴桃属的超级泛基因组。我们在这些基因组中鉴定出了大量的结构变异（SVs，包括基因拷贝数变异）和高度分化的区域。值得注意的是，在不同材料的 和 基因的内含子区域内观察到了显著的SV变异性，表明它们在影响果实大小和毛状体形成方面的潜在作用。有趣的是，我们的研究结果表明两个单倍型基因组之间存在高度的遗传分化，其中一个个体暂定为 ，来自 组。这个可能具有杂合基因组的杂种表现出与抗细菌性溃疡病相关的显著遗传适应性，特别是在被 pv. 感染后，通过上调含有特定SV的 基因来实现。此外，我们还讨论了猕猴桃属的种间杂交和分类处理。总体而言，这里构建的综合泛基因组以及我们的研究结果，为研究遗传组成和标记，特别是与SVs相关的标记，奠定了基础，以促进旨在培育猕猴桃所需表型的杂交育种。
