De novo sequencing and transcriptome analysis of a low temperature tolerant Saccharum spontaneum clone IND 00-1037
| Autor: | Ravinder Kumar, Bakshi Ram, S. Dharshini, M. Chakravarthi, V. M. Manoj, Chinnaswamy Appunu, J. Ashwin Narayan, M. R. Meena, M Naveenarani |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
clone (Java method) Bioengineering Applied Microbiology and Biotechnology Transcriptome 03 medical and health sciences Gene expression Botany De novo sequencing Cluster Analysis KEGG Gene Cold stress Plant Proteins Genetics biology Gene Expression Profiling Saccharum spontaneum General Medicine biology.organism_classification Saccharum Cold Temperature 030104 developmental biology Metabolic Networks and Pathways Biotechnology |
| Zdroj: | Journal of biotechnology. 231 |
| ISSN: | 1873-4863 |
| Popis: | Saccharum spontaneum L., a wild relative of sugarcane, is known for its adaptability to environmental stresses, particularly cold stress. In the present study, an attempt was made for transcriptome profiling of the low temperature (10°C) tolerant S. spontaneum clone IND 00-1037 collected from high altitude regions of Arunachal Pradesh, North Eastern India. The Illumina Nextseq500 platform yielded a total of 47.63 and 48.18 million reads corresponding to 4.7 and 4.8 gigabase pairs (Gb) of processed reads for control and cold stressed (10°C for 24h) samples, respectively. These reads were de novo assembled into 214,611 unigenes with an average length of 801bp. Further, all unigenes were aligned to GO, KEGG and COG databases in order to identify novel genes and pathways responsive upon low temperature conditions. The differential gene expression analysis revealed that about 2583 genes were upregulated and 3302 genes were down regulated during the stress. This is perhaps the comprehensive transcriptome data of a low temperature tolerant clone of S. spontaneum. This study would aid in identifying novel genes and also in future genomic studies pertaining to sugarcane and its wild relatives. |
| Databáze: | OpenAIRE |
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