Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data

C. Muñoz, A. Di Genova, A. Maass, A. Orellana, P. Hinrichsen, A. Aravena

Resultado de la investigación: Chapter

Resumen

Grapevine (Vitis spp.) is the most widely cultivated and economically important fruit crop. Even though the genus exhibits a huge diversity present in more than 50 species, the main products are derived from Vitis vinifera whose origin is from the Southern Caucasus to central Europe. Besides, grapevine constitutes per se a model for the study of woody species. In the Southern hemisphere, Chile has become a large wine producer and the main exporter of table grapes. Our present aim is to develop a bioinformatic platform able to identify SNPs, detect splicing variants and annotate new genes, all tools that could finally give support to select traits of interest. We analyzed data from 18 Vitis species, including cultivars of V. vinifera and wild species of the Vitis genus. The data was obtained by Illumina sequencing 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 cv. 'Corvina' while the latter from 'Pinot Noir', 'Inbred Pinot Noir' and 15 other cultivated cultivars and wild species. The sequence reads were aligned onto the 12X draft sequence of the 'Pinot Noir'-derived 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. Preliminary results detected 387,278 putative SNPs using a Q-score of 20, coverage over 8x and a variability of over 25%. This study will help to improve the current Vitis genome annotation as well as to increase our knowledge about Vitis phylogenetic relationships. Our next step will be to search for new genes as well as spliced variants within Vitis genus. Future perspectives involve the integration of transcriptomic and proteomic data.

Idioma originalEnglish
Título de la publicación alojadaX International Conference on Grapevine Breeding and Genetics
EditorialInternational Society for Horticultural Science
Páginas349-356
Número de páginas8
ISBN (versión digital)9789462610347
DOI
EstadoPublished - 20 jul 2014

Serie de la publicación

NombreActa Horticulturae
Volumen1046
ISSN (versión impresa)0567-7572

Huella dactilar

Vitis
Vitis vinifera
genome
single nucleotide polymorphism
Sciaenidae
table grapes
alternative splicing
fruit crops
cultivars
transcriptomics
bioinformatics
Central European region
proteomics
Chile
wines
genes
RNA
phylogeny

ASJC Scopus subject areas

  • Horticulture

Citar esto

Muñoz, C., Di Genova, A., Maass, A., Orellana, A., Hinrichsen, P., & Aravena, A. (2014). Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data. En X International Conference on Grapevine Breeding and Genetics (pp. 349-356). (Acta Horticulturae; Vol. 1046). International Society for Horticultural Science. https://doi.org/10.17660/ActaHortic.2014.1046.47
Muñoz, C. ; Di Genova, A. ; Maass, A. ; Orellana, A. ; Hinrichsen, P. ; Aravena, A. / Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data. X International Conference on Grapevine Breeding and Genetics. International Society for Horticultural Science, 2014. pp. 349-356 (Acta Horticulturae).
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Muñoz, C, Di Genova, A, Maass, A, Orellana, A, Hinrichsen, P & Aravena, A 2014, Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data. En X International Conference on Grapevine Breeding and Genetics. Acta Horticulturae, vol. 1046, International Society for Horticultural Science, pp. 349-356. https://doi.org/10.17660/ActaHortic.2014.1046.47

Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data. / Muñoz, C.; Di Genova, A.; Maass, A.; Orellana, A.; Hinrichsen, P.; Aravena, A.

X International Conference on Grapevine Breeding and Genetics. International Society for Horticultural Science, 2014. p. 349-356 (Acta Horticulturae; Vol. 1046).

Resultado de la investigación: Chapter

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AU - Muñoz, C.

AU - Di Genova, A.

AU - Maass, A.

AU - Orellana, A.

AU - Hinrichsen, P.

AU - Aravena, A.

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AB - Grapevine (Vitis spp.) is the most widely cultivated and economically important fruit crop. Even though the genus exhibits a huge diversity present in more than 50 species, the main products are derived from Vitis vinifera whose origin is from the Southern Caucasus to central Europe. Besides, grapevine constitutes per se a model for the study of woody species. In the Southern hemisphere, Chile has become a large wine producer and the main exporter of table grapes. Our present aim is to develop a bioinformatic platform able to identify SNPs, detect splicing variants and annotate new genes, all tools that could finally give support to select traits of interest. We analyzed data from 18 Vitis species, including cultivars of V. vinifera and wild species of the Vitis genus. The data was obtained by Illumina sequencing 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 cv. 'Corvina' while the latter from 'Pinot Noir', 'Inbred Pinot Noir' and 15 other cultivated cultivars and wild species. The sequence reads were aligned onto the 12X draft sequence of the 'Pinot Noir'-derived 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. Preliminary results detected 387,278 putative SNPs using a Q-score of 20, coverage over 8x and a variability of over 25%. This study will help to improve the current Vitis genome annotation as well as to increase our knowledge about Vitis phylogenetic relationships. Our next step will be to search for new genes as well as spliced variants within Vitis genus. Future perspectives involve the integration of transcriptomic and proteomic data.

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KW - Phylogenetic relationship

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Muñoz C, Di Genova A, Maass A, Orellana A, Hinrichsen P, Aravena A. Vitis vinifera genome annotation improvement using next-generation sequencing technologies and NCBI public data. En X International Conference on Grapevine Breeding and Genetics. International Society for Horticultural Science. 2014. p. 349-356. (Acta Horticulturae). https://doi.org/10.17660/ActaHortic.2014.1046.47