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De novo transcriptome assembly of Vitis flexuosa grapevines inoculated with Elsinoe ampelina

Published online by Cambridge University Press:  16 July 2014

Soon Young Ahn ,
Seon Ae Kim ,
Sung Hwan Jo  and
Hae Keun Yun
Soon Young Ahn
Affiliation:
Department of Horticulture and Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
Seon Ae Kim
Affiliation:
Department of Horticulture and Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
Sung Hwan Jo
Affiliation:
SEEDERS Inc., Daejeon 302-735, Republic of Korea
Hae Keun Yun*
Affiliation:
Department of Horticulture and Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
*
* Corresponding author. E-mail: haekeun@ynu.ac.kr
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Abstract

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers.

Keywords

DEGsshort readstranscriptsVitis
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S130 - S133
Copyright
Copyright © NIAB 2014 

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References

Anders, S and Huber, W (2010) Differential expression analysis for sequence count data. Genome Biology 11: R106.Google Scholar
Chang, S, Puryear, J and Cairney, J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 11: 113–116.Google Scholar
FAOSTAT (2011) Food and agricultural commodities production. Available at http://faostat.fao.org.Google Scholar
Fung, RW, Gonzalo, M, Fekete, C, Kovacs, LG, He, Y, Marsh, E, McIntyre, LM, Schachtman, DP and Qiu, W (2008) Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiology 146: 236–249.CrossRefGoogle Scholar
Garg, R, Patel, RK, Tyagi, AK and Jain, M (2011) De Novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Research 18: 53–63.Google Scholar
Gibbons, JG, Janson, EM, Hittinger, CT, Johnston, M, Abbot, P and Rokas, A (2009) Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Molecular Biology and Evolution 26: 2731–2744.Google Scholar
Jackson, BG, Schnable, PS and Aluru, S (2009) Parallel short sequence assembly of transcriptomes. BMC Bioinformatics 10(Suppl. 1): S14.Google Scholar
Lijavetzky, D, Cabezas, JA, Ibáñez, A, Rodríguez, V and Martínez-Zapater, JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genome 8: 424.Google Scholar
Lodhi, MA, Daly, MJ, Ye, GN, Weeden, NF and Reisch, BI (1995) A molecular marker based linkage map of Vitis . Genome 38: 786–794.Google Scholar
Pearson, RC and Goheen, AC (1998) Compendium of Grape Disease. Saint Paul, Minnesota: APS Press.Google Scholar
Polesani, M, Bortesi, L, Ferrarini, A, Zamboni, A, Fasoli, M, Zadra, C, Lovato, A, Pezzotti, M, Delledonne, M and Polverari, A (2010) General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species. BMC Genomics 11: 117.Google Scholar
Venturini, L, Ferrarini, A, Zenoni, S, Tornielli, GB, Fasoli, M, Santo, SD, Minio, A, Buson, G, Tononi, P, Zago, ED, Zamperin, G, Bellin, D, Pezzotti, M and Delledonne, M (2013) De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. BMC Genomics 14: 41.Google Scholar