Vitis vinifera

Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Vitales; Vitaceae; Vitis

Introduction

The majority of the grape varieties are grown in regions with a mild to temperate climate, examples are the countries in the Mediterranean area like Spain, France, Italy, Greece, Turkey. After rice, the second food crop to be fully sequenced genomically is the grape variety Pinot Noir. This grape variety is one of the first vines to be domesticated some 2,000 years ago. The blueprint of the Vitis genome will make it possible to develop new, more resistant varieties that can produce superior wines. Hopes are that this work will lead, in the future, to a new generation of clones with inducted resistance to main grape diseases that will dramatically cut the amount of chemical still needed for effective and economically sound results.

The grape has a relatively small genome for a crop plant, similar to that of rice or poplar trees and much smaller than that of wheat or maize. Nevertheless, sequencing the genome was complicated by the degree of heterozygosity between pairs of chromosomes, some 11.2% of the sequence differing between homologous regions. Existing software and strategies were not adequate for the assembly of this highly heterozygous genome. Therefore, focus was largely on developing novel algorithms to address this challenge. The genome of the grape is spread over 19 pairs of chromosomes and is around 504.6 megabases in length. A total coverage of seven genome equivalents of libraries of ascending size sequenced by the Sanger method, coupled with systematic highly parallel automated primer walking and 4.2 genome equivalents of 454 Life ScienceTM sequences, allowed to create an effective genome sequence. Assembly was then reached by adding sequences of two BAC-libraries and a fosmid library which were end-sequenced to assemble large meta-contigs. Contigs were oriented and ordered on appropriate chromosomes by high throughput marker development and genotyping. Currently, 59,883 contigs merged into 705 meta-contigs organised in 19 chromosomes covering 534,5 Mb have been submitted to the GenBank and EBI databases.

Our involvement

While for many organisms we are involved in the gene annotation of the genome, here we are partner to elucidate the evolutionary history of the species. The achieve this we're applying sophisticated software (i-ADHoRe) to detect duplicated segments. Also making Ks-age distributions is a part of our analysis.

In collaboration with:



Publications

2015

Potenza, E., Luisa Racchi, M., Sterck, L., Coller, E., Asquini, E., Tosatto, S.C. E., Velasco, R., Van de Peer, Y., Cestaro, A. (2015) Exploration of alternative splicing events in ten different grapevine cultivars. BMC Genomics 16:706 .

2007

Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., FitzGerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J., Sterck, L., Vandepoele, K., Grando, M.S., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F., Viola, R. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLoS One 2(12):e1326.











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