title: De novo transcriptome assembly of two contrasting pumpkin cultivars.
abstract: Cucurbita pepo (squash, pumpkin, gourd), a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq) of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, 'Big Moose' with large round fruits and 'Munchkin' with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882) and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883) sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively), which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for 'Big Moose' and 'Munchkin' were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses.
authors.affiliation: Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 57001, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece.
authors.forename: Aliki
authors.initials: A
authors.lastname: Xanthopoulou
authors.affiliation: Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Fotis
authors.initials: F
authors.lastname: Psomopoulos
authors.affiliation: Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 57001, Greece.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Ganopoulos
authors.affiliation: Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania Crete, Greece.
authors.forename: Maria
authors.initials: M
authors.lastname: Manioudaki
authors.affiliation: Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 57001, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Tsaftaris
authors.affiliation: Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece.
authors.forename: Irini
authors.initials: I
authors.lastname: Nianiou-Obeidat
authors.affiliation: Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 57001, Greece.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Madesis
keywords: Contrasting cultivars; Cucurbita pepo; Pumpkin; RNA-Seq