Areas of specific Research
The center has strong on-going programs in frontier areas of plant research such as genome mining, molecular mapping, stress biology and nutritional genomics for crop improvement, contributing towards development of improved varieties for high yields. With recent explosion of biomolecular data (genomes, transcriptomes, epigenomes, proteomes and other - omics data from diverse cells, tissues and organisms) from Next Generation Sequencing (NGS) and high throughput (HTP) proteomic experiments, generation and analysis of large datasets now constitutes a routine and significant portion of research at NIPGR.
The BTISNET Coordinator's group works in the area of transcriptional regulation of gene expression, the main focus being the Mediator complex. The group has made substantial advances in understanding the organisation of subunits in the complex and flexibility of the complex. The coordinator's group has also interest in genomics of rice and Arabidopsis. The Co-coordinator's group is exploring several new areas in plant genome research including identification, characterization and validation of novel molecules by analysing high throughput sequencing datasets. His choice of molecules includes transfer RNA-derived fragments (e.g. tRFs), fusion transcripts, circular RNAs and ribosomal RNA-derived fragments (e.g. rRFs). In addition to this, they are also developing in silico tools, pipelines, web-servers and databases for biological research community.
Current Research Heighlights
- We analysed the disorder of Mediator complex and explained the flexibility of the overall structure of the complex. This is a significant contribution in the field of Mediator.
- We explored the arrangement of subunits in the Mediator complex of Arabidopsis. As structure of plant Mediator complex is not yet solved, this paper is a significant contribution in understanding the structure function of plant Mediator.
- Whole genome sequences of four rice accession were analysed. This helped in identification of three novel grain size/weight QTLs.
- We have characterized a low diversity region around the centromeric region of chromosome 5 of rice. This is significant study in understanding the domestication of rice.
- We are studying two novel molecules in planta e.g. Transfer RNA-derived fragments (tRFs) and fusion transcripts.
- We did an extensive data curation and identified all three kind of tRFs (e.g. tRF-5, tRF-3 and tRF-1) for 10 different plants species (study published).We have also developed a software package for the identification of tRFs. We have also identified and analyzed tRFs in Rice, tomato and chickpea at different stress conditions.
- Fusion transcripts are chimeric RNAs generated due to fusion either at DNA or RNA level. Those transcripts may either act as long non-coding RNAs or encode novel chimeric proteins. We started the work by identifying fusion transcripts in paired-end RNA-Seq datasets of Arabidopsis thaliana.
- First databases of Plant tRFs, tRNAs, and fusion transcripts developed by our group.
- Developed the methodology for the identification of tRFs in small RNA sequencing datasets e.g. tRF-PRED: Software package for the prediction of tRFs.
