Plant Molecular Biology

, Volume 84, Issue 1, pp 159–171

De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers

  • Shalini Mudalkar
  • Ramesh Golla
  • Sreenivas Ghatty
  • Attipalli Ramachandra Reddy
Article

DOI: 10.1007/s11103-013-0125-1

Cite this article as:
Mudalkar, S., Golla, R., Ghatty, S. et al. Plant Mol Biol (2014) 84: 159. doi:10.1007/s11103-013-0125-1

Abstract

Camelina sativa L. is an emerging biofuel crop with potential applications in industry, medicine, cosmetics and human nutrition. The crop is unexploited owing to very limited availability of transcriptome and genomic data. In order to analyse the various metabolic pathways, we performed de novo assembly of the transcriptome on Illumina GAIIX platform with paired end sequencing for obtaining short reads. The sequencing output generated a FastQ file size of 2.97 GB with 10.83 million reads having a maximum read length of 101 nucleotides. The number of contigs generated was 53,854 with maximum and minimum lengths of 10,086 and 200 nucleotides respectively. These trancripts were annotated using BLAST search against the Aracyc, Swiss-Prot, TrEMBL, gene ontology and clusters of orthologous groups (KOG) databases. The genes involved in lipid metabolism were studied and the transcription factors were identified. Sequence similarity studies of Camelina with the other related organisms indicated the close relatedness of Camelina with Arabidopsis. In addition, bioinformatics analysis revealed the presence of a total of 19,379 simple sequence repeats. This is the first report on Camelina sativa L., where the transcriptome of the entire plant, including seedlings, seed, root, leaves and stem was done. Our data established an excellent resource for gene discovery and provide useful information for functional and comparative genomic studies in this promising biofuel crop.

Keywords

De novo assembly Camelina Transcriptome SSRs Biofuel 

Supplementary material

11103_2013_125_MOESM1_ESM.xlsx (2.2 mb)
Supplementary material 1 (XLSX 2236 kb)
11103_2013_125_MOESM2_ESM.xlsx (3.4 mb)
Supplementary material 2 (XLSX 3451 kb)
11103_2013_125_MOESM3_ESM.xlsx (1.7 mb)
Supplementary material 3 (XLSX 1712 kb)
11103_2013_125_MOESM4_ESM.xlsx (1.8 mb)
Supplementary material 4 (XLSX 1870 kb)
11103_2013_125_MOESM5_ESM.xlsx (67 kb)
Supplementary material 5 (XLSX 66 kb)
11103_2013_125_MOESM6_ESM.xlsx (25 kb)
Supplementary material 6 (XLSX 24 kb)
11103_2013_125_MOESM7_ESM.xlsx (16 kb)
Supplementary material 7 (XLSX 16 kb)
11103_2013_125_MOESM8_ESM.xlsx (67 kb)
Supplementary material 8 (XLSX 67 kb)
11103_2013_125_MOESM9_ESM.xlsx (33 kb)
Supplementary material 9 (XLSX 33 kb)
11103_2013_125_MOESM10_ESM.xlsx (11 kb)
Supplementary material 10 (XLSX 10 kb)
11103_2013_125_MOESM11_ESM.doc (46 kb)
Supplementary material 11 (DOC 45 kb)

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Shalini Mudalkar
    • 1
  • Ramesh Golla
    • 1
  • Sreenivas Ghatty
    • 2
  • Attipalli Ramachandra Reddy
    • 1
  1. 1.Department of Plant SciencesUniversity of HyderabadHyderabadIndia
  2. 2.Tree Oils India LimitedZaheerabadIndia

Personalised recommendations