Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Roach, Michael J.; Johnson, Daniel L.; Bohlmann, Jöerg; Vuuren, H. J. J. Van; Jones, Steven J.M.; Pretorius, Isak S.; Schmidt, Simon A.; Borneman, Anthony R.

doi:10.1101/389197

Cited by 34 publications

(41 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, advanced techniques were used to successfully sequence the genome of an interspecific table grape hybrid. Sequence contiguity and quality, which were supported by N50 length and BUSCO analysis, respectively (Table 1), compared favorably with those of the reported grapevine genomes (Canaguier et al 2017;Chin et al 2016;Jaillon et al 2007;Minio, Massonnet, Figueroa-Balderas, Castro, et al 2019;Roach et al 2018;Velasco et al 2007;Vondras et al 2019;Zhou et al 2018).…”

Section: Discussionsupporting

confidence: 58%

“…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). However, genome sequences for table grapes, which are often derived from interspecific hybrids, have not been available to date.…”

Section: Discussionmentioning

confidence: 99%

“…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' . In parallel,…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Shirasawa

Azuma

Taniguchi

et al. 2019

Preprint

View full text Add to dashboard Cite

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'.

show abstract

Section: Discussionsupporting

confidence: 58%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Shirasawa

Azuma

Taniguchi

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Nucmer tool (from MUMmer tool: https://sourceforge.net/projects/mummer/ - nucmer (version 3.1) parameters: -maxmatch –l 100 -c 500) and the grapevine reference genome 8 (PN40024, version 12X.2 - https://urgi.versailles.inra.fr/Species/Vitis/Data-Sequences/Genome-sequences) were used to align the Sylvestris assembly to the PN40024 reference assembly in order to see completeness of this Sylvestris assembly. Nucmer and grapevine reference genome were also used to anchor and order Sylvestris contigs into chromosomes (with additional parameters –r –q), as it was done in the Chardonnay genome assembly paper 34 .…”

Section: Supplementary Informationmentioning

confidence: 99%

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Badouin

Velt

Gindraud

et al. 2020

Preprint

View full text Add to dashboard Cite

Grapevine has a major economical and cultural importance since antiquity. A key step 27! in domestication was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. 28! sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. vinifera. 29! While the grapevine sex locus is known to be small, its precise boundaries, gene content 30! and the sex-determining genes are unknown. Here we obtained a high-quality de novo 31! reference genome for V. sylvestris and whole-genome resequencing data of a cross. 32!Studying SNP segregation patterns, gene content and expression in wild and cultivated 33! accessions allowed us to build a model for sex determination in grapevine. In this model, 34! up-and down-regulation of a cytokinin regulator is sufficient to cause female sterility 35! and reversal to hermaphroditism, respectively. This study highlights the importance of 36! neo-functionalization of Y alleles in sex determination and provides a resource for 37! studying genetic diversity in V. sylvestris and the genomic processes of grapevine 38! domestication. 39! 40! Dioecy is rare in flowering plants (~6%) but over-represented among crops (~20%) 1 . In some 41! cases, both wild and cultivated plants are dioecious (e.g. date palm, asparagus, persimmons). 42! Other crops, such as grapevine, papaya, and strawberry, derive from dioecious progenitors 43! and switched to hermaphroditism during domestication. The genes underlying this switch are 44! currently not known in any crop. In Vitis sylvestris, wild females produce morphologically 45! bisexual flowers, with retracted anthers that produce few and infertile pollen 2 , while male 46! flowers undergo early ovule abortion 3 . Genetic analyses identified a 143-kb haplotype 47! responsible for sex-determination in the grapevine reference genome 4,5 . Two candidate genes 48! for female sterility have been proposed, in particular APRT3 6 , a putative cytokinin regulator. 49! ! 3! ! However, the sequence of the sex locus was not available in V. sylvestris and no causative 50! mutations have been identified. A genetic and evolutionary model to explain sex 51!determination and switch to hermaphroditism in grapevine is currently lacking. 52!We sequenced a female individual of V. sylvestris using SMRT-sequencing (120X). Contigs 53!were assembled with falcon-unzip 7 and the grapevine reference genome 8 (PN40024 -version 54! 12X.2) was used to build pseudomolecules. We obtained a high-quality diploid assembly of 55! 469 Mb with a contig N50 of 1.7 Mb, 98% of the gene content anchored on chromosomes and 56! a BUSCO evaluation of 95% (Supplementary Table 1, Supplementary Figure 1), comparing 57! favorably to other recently published plant genomes 9,10 . We annotated 39,031 protein-coding 58! genes on primary contigs. 59!To study sex determination, we localized the sex locus, which was fully included in the 5 th 60! largest contig of the assembly. We also sequenced and assembled bacterial artificial 61! chromosomes (BACs) cover...

show abstract

“…The total p-contig size was larger than the estimated genome size of V. vinifera (∼500 Mbp) suggesting that in some cases FALCON-Unzip underestimated the alternative haplotype sequences because of high heterozygosity between homologous regions, which is common in grapevine 13 14 . 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 .…”

Section: Background and Summarymentioning

confidence: 99%

De novo phased assembly of the Vitis riparia grape genome

Girollet

Rubio

Bert

2019

Preprint

View full text Add to dashboard Cite

show abstract

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Cited by 34 publications

References 75 publications

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

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

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

De novo phased assembly of the Vitis riparia grape genome

Contact Info

Product

Resources

About