A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

Abstract

A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3

Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)

“…The boundaries of the sex determination region were determined by mapping the coding sequences (CDS) of the chr02:4840000 -498000 region from PN40024 12X.v2 (Canaguier et al, 2017) to the Char04 and Cab08 references. For both Chardonnay and Cabernet Sauvignon haplotypes, gene models were refined by mapping all the CDS identified in the four haplotypes onto Char04 and Cab08 genome assemblies, separately, using GMAP v.2015-11-20 with default parameters (Wu and Watanabe, 2005).…”

“…To identify whether other green berry accessions housed large inversions that include the berry color genes, we determined the orientation of the rearranged chromosome fragments and putative breakpoints from bam files of discordant PE reads and split reads (SP) after mapping short-reads to the PN40024 genome V2.0 (Canaguier et al, 2017). Reads were mapped using the BWA-MEM algorithm in bwa-0.7.12 (Li, 2014).…”

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

“…vinifera PN40024) (Canaguier et al 2017;Jaillon et al 2007). Subsequent advances in sequencing technologies allowed in-depth analysis of heterozygous genomes in some wine grape cultivars (Chin et al 2016;Minio, Massonnet, Figueroa-Balderas, Castro, et al 2019;Roach et al 2018;Zhou et al 2018).…”

“…vinifera 'Pinot Noir' (version 12X) (Canaguier et al 2017). This analysis confirmed that VSMuph_r1.0 and VSMph_r1.0 completely encompassed the reference sequence of the V. vinifera genome ( Figure 2B and 2C), and confirmed the doubled size of VSMph_r1.0 ( Figure 2C).…”

“…The original genome project used a V. vinifera cultivar, 'Pinot Noir'. Since the original genome publication, the 'Pinot Noir' genome sequence data has been updated and the last version was released in 2017 (Canaguier et al 2017). In addition, to our knowledge, de novo genome sequence assemblies have been released for four wine cultivars of V. vinifera: 'Cabernet Sauvignon' (Chin et al 2016;Minio, Massonnet, Figueroa-Balderas, Vondras, et al 2019;Minio et al 2017), 'Carménère' (Minio, Massonnet, Figueroa-Balderas, Castro, et al 2019), 'Chardonnay' (Zhou et al 2018;Roach et al 2018), and 'Zinfandel' .…”