Hortic Res Highlights 2024 | Kiwifruit T2T Reference Genome Kiwifruit Is An Emerging Vine Fruit Tree With Important Economic Value.

Its fruit has an extremely high vitamin C content and is known as the "king of fruits". China is the origin and distribution center of kiwifruit and also the country with the largest cultivated area and yield of kiwifruit. The assembly and annotation of high-quality reference genomes have important theoretical significance and application value for functional genomics research on important agronomic traits of kiwifruit and whole-genome molecular design breeding. In January 2023, "Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis" completed by the College of Horticulture of Anhui Agricultural University in cooperation with multiple institutions including the Shenzhen Agricultural Genomics Research Institute of the Chinese Academy of Agricultural Sciences, the Institute of Fruit and Tea Research of the Hubei Academy of Agricultural Sciences, and the Institute of Special Animal and Plant Sciences of the Chinese Academy of Agricultural Sciences was published online in Horticulture Research.

This study used PacBio HiFi, ONT ultra-long, and Hi-C sequencing data and combined with a self-developed genome assembly script pipeline to perform a telomere-to-telomere (T2T) de novo assembly of Actinidia chinensis 'Hongyang' (A. chinensis cv. Hongyang), the material for the first kiwifruit genome sequencing. A completely continuous, gap-free high-quality genome was obtained. Following the version number sequence of the existing kiwifruit reference genome, this T2T genome is called 'Hongyang v4.0' (Figure 1). Compared with Hongyang v3.0, Hongyang v4.0 filled all 646 gaps unassembled in Hongyang v3.0, identified the centromeres (Ach-CEN153) of all 58 chromosomes, assembled all other telomeres except for one end of a chromosome (the unassembled telomere may be due to the influence of the acrocentric chromosome), obtained about 40 Mb of new chromosome sequences, and corrected possible assembly errors in historical versions. At the same time, this version achieved haplotype assembly, named HY4P and HY4A (where P and A are the first letter abbreviations of haplotype primary and alternate), and the quality and accuracy of each haplotype assembly are better than the existing kiwifruit genome assemblies. The BUSCO evaluation values are as high as 99.3%. The final assembled sequence sizes are 606.1 and 599.6 Mb respectively, and 45,809 and 45,434 protein-coding genes were annotated.

The completion of the kiwifruit T2T reference genome is a major milestone in kiwifruit genome sequencing research, the ultimate goal of genome assembly, and also the most complete kiwifruit genome sequence to date. The high-quality T2T genome can not only explore the centromere region that has always been called the "genomic black hole", but also discover structural variations at the chromosome level and provide a better reference sequence for downstream gene annotation, providing basic data for molecular breeding and genetic improvement of kiwifruit.