Metagenomics of Plant Rhizosphere
We have started programs which cover the environmental monitoring of UNESCO World HERITAGE Site – The Sunderbans. This project is in collaboration with Dr. Sabdar Rahaman of Bangabasi Evening College and is being funded by West Bengal Department of Science and Technology. In this work Dr. Sayak Ganguli is collaborating with the P.I. and is responsible for the collection of samples and metagenomic sequencing of the rhizosphere of Ferns of the Mangrove forests.
Ganguli, S., Rahaman, S., Bera, A. R., Vishal, V., Malik, S., Roopalakshmi, K., & Singh, P. K. (2017). Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans. Genomics Data, 14, 53–55. http://doi.org/10.1016/j.gdata.2017.09.001/
Metagenomics of Root Endophytic Microbiome
Root endophytic microbiomes represent one of the most unexplored biomes of plant members. Yet they are vital cogs in the entire soil – plant – environment continuum. AIIST has collaborated with Dr. Subhadeepa Sengupta from the Department of Botany, Bidhannagar College, Kolkata in exploring the root endophytic microbiome of one of the principal crops of the Indian subcontinent -Rice (Oryza sativa L.). The finding have been published.
Subhadipa Sengupta, Sayak Ganguli, Pankaj K Singh (2017): Metagenome analysis of the root endophytic microbial community of Indian rice (O. sativa L.). Genomics Data 02/2017; 12., DOI: 10.1016/j.gdata.2017.02.010
Transcriptome Analyses from Plants
Sequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq) has in the past few years displayed remarkable potential to unravel unprecedented complexity of the plant transcriptomes. The transcriptome sequencing of plants provides quick insights into the gene space, opportunity to isolate genes of interest, development of functional markers, quantification of gene expression, and comparative genomic studies. In the past two years the theoretical and computational biology unit of AIIST has collaborated with Prof. Amita Pal, of the Division of Plant Biology, Bose Institute, Kolkata for unraveling the patterns in transcriptome data of Vigna mungo (black gram). Various sequencing libraries have been submitted to the NCBI-SRA archive and work is in full swing to decipher the complexities.
Sayak Ganguli, Avishek Dey, Rahul Banik, Anirban Kundu, Amita Pal: Analyses of MYMIV-induced transcriptome in Vigna mungo as revealed by next generation sequencing. Genomics Data 01/2016; 7(C)., DOI:10.1016/j.gdata.2016.01.005 {Featured Article of Lab Resource Segment).
NCBI - SRA Submissions
- BIOPROJECT ID: PRJNA288413; BIOSAMPLE: SAMN03799418; SRA ACCESSION: SRX1058325; SRX1058327.Study Title: Transcriptome Library of Mock Inoculated Vigna mungo cultivar T9; 1 LS454 (454 GS FLX+) run: 32.7M spots, 9.9G bases, 4.6Gb downloads. Study Title: Transcriptome Data of Vigna mungo Cv. T9 infected with MYMIV; 1 LS454 (454 GS FLX+) run: 30.6M spots, 9.2G bases, 4.3Gb downloads.
- BIOPROJECT ID: PRJNA283940; BIOSAMPLE: SAMN03658143; SRA ACCESSION: SRX1032950; SRX1082731 Study Title: Transcriptome Library of Vigna mungo RIL VM84 infected with MYMIV; 1 LS454 (454 GS FLX) run: 56.1M spots, 11.3G bases, 6.8Gb downloads. Study Title: Transcriptome Library of mock inoculated Vigna mungo RIL VM84; 1 LS454 (454 GS FLX) run: 39.7M spots, 8G bases, 4.8Gb downloads.