Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.
Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China.
Sci Data. 2023 Feb 14;10(1):92. doi: 10.1038/s41597-023-02006-4.
The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. 'Red5' and 'Hongyang' (11.1-27.7 mya) was more recent compared with the divergence time of them and Acd (19.9-41.2 mya), with the divergence time of A. eriantha cv. 'White' being the earliest (22.9-45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd.
最商业化的猕猴桃品种，中华猕猴桃（Actinidia chinensis var. deliciosa），是一种异源六倍体（2n=6x=174），这使得高质量组装基因组具有挑战性。我们之前发现了一种罕见的天然二倍体中华猕猴桃植物。在这里，报告了这种二倍体中华猕猴桃的染色体水平从头基因组组装，长度约为 621.98 Mb，其 Contig 和 Scaffold N50 值分别为 10.08 和 21.09 Mb，99.66%的碱基锚定在 29 条假染色体上，注释了 38990 个蛋白质编码基因和 42.29%的重复元件。A. chinensis cv. 'Red5' 和 'Hongyang'（11.1-27.7 mya）与 Acd（19.9-41.2 mya）的分化时间比 A. chinensis cv. 'Red5' 和 'Hongyang'（11.1-27.7 mya）的分化时间更近，而 A. eriantha cv. 'White'（22.9-45.7 mya）的分化时间是四个猕猴桃物种中最早的。4DTv 距离分布突出了 Acd 中最近发生的三次全基因组复制事件。这是第一个高质量的二倍体中华猕猴桃基因组，不仅为猕猴桃功能基因组学研究奠定了重要基础，也进一步阐明了异源六倍体 Acd 的基因组进化。
