| Title |
Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass
|
|---|---|
| Published in |
Plant Cell Reports, November 2016
|
| DOI | 10.1007/s00299-016-2065-0 |
| Pubmed ID | |
| Authors |
Vasudevan Ayyappan, Malay C. Saha, Jyothi Thimmapuram, Venkateswara R. Sripathi, Ketaki P. Bhide, Elizabeth Fiedler, Rita K. Hayford, Venu (Kal) Kalavacharla |
| Abstract |
Transcriptomes of two switchgrass genotypes representing the upland and lowland ecotypes will be key tools in switchgrass genome annotation and biotic and abiotic stress functional genomics. Switchgrass (Panicum virgatum L.) is an important bioenergy feedstock for cellulosic ethanol production. We report genome-wide transcriptome profiling of two contrasting tetraploid switchgrass genotypes, VS16 and AP13, representing the upland and lowland ecotypes, respectively. A total of 268 million Illumina short reads (50 nt) were generated, of which, 133 million were obtained in AP13 and the rest 135 million in VS16. More than 90% of these reads were mapped to the switchgrass reference genome (V1.1). We identified 6619 and 5369 differentially expressed genes in VS16 and AP13, respectively. Gene ontology and KEGG pathway analysis identified key genes that regulate important pathways including C4 photosynthesis, photorespiration and phenylpropanoid metabolism. A series of genes (33) involved in photosynthetic pathway were up-regulated in AP13 but only two genes showed higher expression in VS16. We identified three dicarboxylate transporter homologs that were highly expressed in AP13. Additionally, genes that mediate drought, heat, and salinity tolerance were also identified. Vesicular transport proteins, syntaxin and signal recognition particles were seen to be up-regulated in VS16. Analyses of selected genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, membrane transporters, heat, drought and salinity stress responses confirmed significant variation in the relative expression reflected in RNA-Seq data between VS16 and AP13 genotypes. The phenylpropanoid pathway genes identified here are potential targets for biofuel conversion. |
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Mexico | 1 | 20% |
| France | 1 | 20% |
| Unknown | 3 | 60% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 60% |
| Scientists | 2 | 40% |
Mendeley readers
The data shown below were compiled from readership statistics for 34 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 3% |
| Unknown | 33 | 97% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 13 | 38% |
| Student > Ph. D. Student | 7 | 21% |
| Professor > Associate Professor | 3 | 9% |
| Student > Bachelor | 2 | 6% |
| Student > Master | 2 | 6% |
| Other | 5 | 15% |
| Unknown | 2 | 6% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 19 | 56% |
| Biochemistry, Genetics and Molecular Biology | 5 | 15% |
| Computer Science | 3 | 9% |
| Environmental Science | 1 | 3% |
| Chemical Engineering | 1 | 3% |
| Other | 2 | 6% |
| Unknown | 3 | 9% |
Attention Score in Context
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#14,431,072
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#1,634
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#173,646
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Outputs of similar age from Plant Cell Reports
#17
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