Genomics

The genomic and DNA fingerprinting unit is established to provide technical and analytical support for molecular biology and genomics research  under AMAAS at the NBAIM. The goal is  to perform  Reference and de novo draft Genome Sequencing of  potential AIMS and their functional annotation as well as molecular characterization and identification of agriculturally important microorganisms. The unit is equipped with the equipments and facilities for DNA library preparation, DNA sequencing (Sanger and Next Generation 454 pyrosequencing), fragment analysis, quantitative PCR. The facility is available to scientists of NBAIM as well as researchers from NARS system/other research collaborators with due approval of competent authority/ Director NBAIM.  
 
The unit has ABI  3130 xl Genetic Analyzer, the latest generation of 16 capillary electrophoresis instruments being used for  a wide variety of sequencing and fragment analysis applications including  the signature gene sequencing and microsatellite analysis. The full range of applications can be run on a single polymer and capillary array meaning you can run mixed applications on one plate. For large projects the unit has 454 Sequencing, that  is a Next-Generation Sequencing technology.  In this the data is generated using pyrosequencing chemistry where clonally amplified libraries are sequenced by synthesis.  Libraries are prepared using emulsion-based PCR (emPCR) amplification on beads.  Each bead occupies a well on a Pico-Titer-Plate or PTP plate and the nucleotides in the sequence are determined by a chemiluminescent signal occurring during nucleotide incorporation.  This signal is captured by a high resolution camera and is proportional to the number of nucleotides incorporated.  The signals are processed and sequence is determined. A single run produces up to 1 million sequence reads that are on average 400bp, and will soon approach 800bp.  For additional flexibility, runs can be multiplexed bioinformatically through the use of barcoding or MID (Multiplex Identifiers) adapters, or physically through the use of 2, 4, 8 or 16-region gaskets. The throughput and read lengths offered by this system make it an ideal platform for:
 
  • Whole-genome sequencing of small or medium genomes
  • Amplicon Sequencing
  • Transcriptome sequencing
  • Targeted Resequencing
  • Metagenomics