Abstract
Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. The high-quality assembled genome is 653 Mb long, with 0.76% heterozygosity. At least 43% of the genome consists of repetitive sequences, and the most abundant long terminal repeats were further identified and account for 23.38% of our novel genome. It has clear improvements in contiguity, accuracy, and gene annotation over the two previous versions and contains 40,464 annotated protein-coding genes, of which 94.41% are functionally annotated. Moreover, further analyses of genetic collinearity revealed that the kiwifruit genome has undergone two whole-genome duplications: one affecting all Ericales families near the K-T extinction event and a recent genus-specific duplication. The reference genome presented here will be highly useful for further molecular elucidation of diverse traits and for the breeding of this horticultural crop, as well as evolutionary studies with related taxa.
Highlights
Kiwifruit is produced by various species of the genus Actinidia (Actinidiaceae)
Most generated scaffolds can be anchored into chromosomes based on interaction frequencies of sequences (Hi-C data), providing highresolution chromosome-level assemblies. We report such a high-quality de novo chromosome-level genome for a heterozygous kiwifruit, ‘Hongyang’, which is widely grown in China; the genome was generated by assembling long PacBio reads and mapping scaffolds based on Hi-C interaction confirmation
We aligned our Illumina and RNA-seq reads to the v3.0 assembly using BWA11, HISAT212 and Blasr[13], which showed good alignments with proper mapping rates of 92.47% and 91.00%, respectively (Supplementary Tables 2 and 3)
Summary
Kiwifruit (known as “the king of fruits” because of its remarkably high concentration of vitamins, minerals, and other nutrients) is produced by various species of the genus Actinidia (Actinidiaceae). More than 50 species of the genus have been described, and more than 60 cultivars are grown throughout the world[1]. Major cultivars have been domesticated or bred from Actinidia chinensis Planchon, with ploidy levels ranging from diploid (2n = 2× = 58) to octoploid. A diploid cultivar of this species was selected to assemble genomes in the present and previous studies. The first released A. chinensis genome[2] (hereafter v1.0) was assembled from short Illumina reads, and the second (of genotype Red[53], hereafter v2.0) was assembled from short Roche 454 reads.
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