conference schedule and program with abstracts - Horticulture ...

P-32
Vitis vinifera genome annotation improvement using next-generation sequencing
technologies and NCBI public data
C. Muñoz 1 , A. Di Genova 2* , A. Maass 2 , A. Orellana 1 , P. Hinrichsen* 3 A. Aravena 2
1 Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile; 2 Centro de
Modelamiento Matemático, Universidad de Chile, Santiago, Chile; 3 INIA La Platina, Santiago,
Chile
*Corresponding author: phinrichsen@inia.cl
Grapevine (Vitis spp.) is the most widely cultivated and economically important fruit crop and
exhibits a huge diversity, comprising more than 50 species. However, the main grape products
are produced solely from Vitis vinifera whose origin is assumed to have been the southern area of
Caucasus Mountains and Caspian Sea. In Chile, grapevine represents the main fruit crop and has
made our country the principal exporter of fresh consumption products in Southern hemisphere.
Moreover, grapevine constitutes per se a model for woody plant species. Our aim is to develop a
national biotechnological platform to support new genome sequencing technologies capabilities
for Chilean grape breeding programs, which will be used in germplasm selection for traits of
interest as well as SNPs, splicing variants, and new gene identification. We analyzed data from
18 species of the Vitis genus, including commercial varieties of Vitis vinifera and wild species of
Vitis genus obtained using Illumina sequencing technology from two RNA-seq experiments
performed by Zenoni et al. (2010) and Myles et al. (2010), both available at NCBI. The first one
reported data from ‘Corvina’ and the latter from ‘Pinot Noir’, inbred ‘Pinot Noir’ and 15 other
cultivated and wild species. The sequence reads were aligned onto the 12X draft sequence of the
‘Pinot Noir 40024’ genome whereas the reported data was aligned onto 8X genome. The
alignments were analyzed to detect alternative splicing events and expressed single nucleotide
polymorphisms (SNPs). We aligned 116,665,608 reads, selecting hits with at most two
mismatches. Over 55% of the reads showed only one alignment to the reference genome, 19%
had multiple matches and 26% of them were unmatched. Our preliminary results detected
387,278 putative SNPs using a Q-score of 20, coverage over 8X, and variability over 25%. This
study will allow us to improve the current Vitis genome annotation as well as increase our
knowledge about Vitis evolutionary phylogenetic relationships. Our next step will be to search
for new genes as well as splice variants within Vitis genus. Our future perspects involve the
integration of our developing experiments from transcriptomics and proteomics approaches.
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