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

Abstract

Little is known about the type and numbers of structural variants (SVs) in plant genomes, the evolutionary processes that shape SV variation, or their effects on phenotypes. Here we assembled the 605Mb genome of the Chardonnay grape (Vitis vinifera ssp. sativa), which we use to catalog SVs within and between genomes and also across 69 cultivars and wild accessions. SVs underlie widespread hemizygosity of protein coding genes within Chardonnay and genic presence-absence variation between cultivars. Negative selection acts against all SV types, but they also accrue as heterozygous, recessive mutations in clonally propagated grapevines. SV hotspots in the sex determination region and the berry color locus illustrate their impact on phenotype and the role of SVs as drivers of convergent phenotypic evolution.3

A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’

“…2). We further compared the 'Concord' AMAT locus with several published contigs of V. vinifera cultivars aligned to the AMAT region 19,28,[30][31][32][33] . Compared to 'Concord', all examined V. vinifera contigs had a 426-bp sequence in their AMAT promoters, which was in contrast with the obersered 400 bp in the reference genome PN40024, suggesting that a 26-bp sequence was absent in PN40024 ( Fig.…”

“…A 3-kb fragment in the promoter region, indicated with an aqua-colored bracket, was deleted in one AMAT allele in 'Chardonnay' clone I10V1 and some other V. vinifera accessions 30,31,33 . Two types of insertions (gray boxes) were found in exon 2 at the exact same position, 504 bp (a soloLTR) in 'Pinot Noir' clone ENTAV 115 19 and 1188 bp (a TRIM with 5′LTR, internal sequence and 3′LTR) in the second AMAT allele of 'Chardonnay' I10V1 and some other accession [29][30][31][32] 414 'Concord' had both A and G while 'Catawba' had only G (Table S14), suggesting that 'Concord' is heterozygous for the AMAT locus with one of the AMAT alleles from 'Catawba'. No major structural variation was found in the ORFs sequenced for these cultivars except 'Caco' which had one allele with a 4 bp frameshift insertion.…”

“…Two V. vinifera reference genomes, based on a nearly homozygous line PN40024 derived from 'Pinot noir' and a highly heterozygous 'Pinot noir' clone ENTAV 115, respectively, were released in 2007 18,19 . Additional Vitis genome projects, mostly involving V. vinifera, have been pursued in the last decade [20][21][22][23][24][25][26][27][28][29][30][31][32][33] . However, no genomes of V. labrusca cultivars have been reported.…”

Diploid Genome Assembly of the Wine Grape Carménère

“…Extensive structural variation between grape genotypes leads to significant unshared gene content between cultivars, which has been shown to contribute to varietal phenotypic characteristics (Venturini et al 2013; Da Silva et al 2013; Gambino et al 2017; Zhou et al 2018; Minio et al 2019). Cultivar-specific genes have been discovered by whole-genome or transcriptome comparative analyses (Venturini et al 2013; Da Silva et al 2013; Gambino et al 2017; Zhou et al 2018; Minio et al 2019). However, despite the relatively small genome size estimated at about 500 Mbp, the assembly of grape genomes is difficult because of the high level of heterozygosity (Minio et al 2017).…”

De novo phased assembly of the Vitis riparia grape genome

“…Later, the PacBio assembly and annotation of V. vinifera cv Chardonnay variety provided after curation of artefactual contig assignment, 854 p-tigs and 1883 h-tigs, totaling 490 Mb and 378 Mb 15 . More recently, another version of the Chardonnay genome was proposed with a different level of curation at 605 Mb 16 .…”