De novo transcriptome assembly of two contrasting pumpkin cultivars

 
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De novo transcriptome assembly of two contrasting pumpkin cultivars

Ganopoulos, Ioannis
Tsaftaris, Athanasios
Nianiou-Obeidat, Irini
Xanthopoulou, Aliki
Manioudaki, Maria
Psomopoulos, Fotis
Madesis, Panagiotis

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 pump- kin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis(RNA-Seq) oftwo contrastingpumpkin cultivars. Leavesand female fl owers of cultivars, ‘ Big Moose ’ with large round fruits and ‘ Munchkin ’ with small round fruits, were harvested for totalRNA extraction.Weobtained 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 14,824,292150-base reads.Afterquality as- sessment, 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 identi fi ed possible coding re- gions 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. © 2016 Published by Elsevier Inc.

Article / Άρθρο
info:eu-repo/semantics/article

Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης (EL)
Aristotle University of Thessaloniki (EN)

Αγγλική γλώσσα

2016
2016-11-11T12:07:15Z


Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης, Σχολή Επιστημών Υγείας, Τμήμα Ιατρικής

Genomics Data, vol.7 no.C [2016] p.200-201
urn:ISSN:22135960

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info:eu-repo/semantics/openAccess



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