| Title |
De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers
|
|---|---|
| Published in |
Plant Molecular Biology, September 2013
|
| DOI | 10.1007/s11103-013-0125-1 |
| Pubmed ID | |
| Authors |
Shalini Mudalkar, Ramesh Golla, Sreenivas Ghatty, Attipalli Ramachandra Reddy |
| 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. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 50% |
| Unknown | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 50% |
| Scientists | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 79 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| India | 1 | 1% |
| United States | 1 | 1% |
| Slovakia | 1 | 1% |
| Unknown | 76 | 96% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 16 | 20% |
| Researcher | 13 | 16% |
| Student > Master | 7 | 9% |
| Student > Doctoral Student | 6 | 8% |
| Student > Bachelor | 5 | 6% |
| Other | 17 | 22% |
| Unknown | 15 | 19% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 39 | 49% |
| Biochemistry, Genetics and Molecular Biology | 11 | 14% |
| Chemistry | 3 | 4% |
| Engineering | 2 | 3% |
| Social Sciences | 2 | 3% |
| Other | 5 | 6% |
| Unknown | 17 | 22% |
Attention Score in Context
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#14,189,417
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Outputs from Plant Molecular Biology
#2,245
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Outputs of similar age from Plant Molecular Biology
#7
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