De novowhole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

Abstract

This study presents the first genome sequence of an interspecific grape hybrid, 'Shine Muscat' (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a "haploid" genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of 'Shine Muscat' was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of 'Shine Muscat' and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the 'Shine Muscat' genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as 'Shine Muscat'.

Simple DNA marker system reveals genetic diversity of MYB genotypes that determine skin color in grape genetic resources

“…Recently, Di Genova et al (2014) reported a draft genome sequence of V. vinifera table grape 'Sultanina' (synonym of 'Thompson Seedless') and identified a large number of structural variants and SNPs in comparison with the reference genome of the wine grape 'Pinot Noir' (line PN40024). Shirasawa et al (2019) reported the de novo whole-genome sequence of interspecific hybrid table grape, 'Shine Muscat', and identified potential structural variants between the genomes of 'Shine Muscat' and 'PN40024'. These differences probably reflect the genetic divergence between table, wine, and rootstock grapes (Aradhya et al 2003).…”

Evidence for high intergenic sequence variation in heterozygous Italian ryegrass (Lolium multiflorumLam.) genome revealed by a high-quality draft diploid genome assembly

“…Despite de novo genome assembly methods are being developed since more than two decades [14], only recently the community started focusing on highly heterozygous genomes [15][16][17][18][19][20][21]. Typically, high amounts of sequence variation between alleles prevent contig extension and scaffolding.…”