Microbial genomics

Genomics: a field of science that analyzes and compares the complete genome (genetic material of an organism) of organisms or a large number of genes in a simultaneous fashion. microbial (Science: biology, microbiology) Pertaining to microorganisms too small to be seen with the naked eye. Microbial genomic : the contact of genomics on our understanding of the microbes life 1) Methods for Studying Microbial Genomes 2) Analysis and Interpretation of Whole Genome Sequences

Why study microbial genomes? analysis of whole microbial genomes also provides insight into microbial evolution and diversity beyond single protein or gene phylogenies in practical terms analysis of whole microbial genomes is also a powerful tool in identifying new applications in for biotechnology and new approaches to the treatment and control of pathogenic organisms Central role in ecological balance Commercial opportunities Pathogens kill millions every year

History of microbial genome sequencing 1977 - first complete genome to be sequenced was bacteriophage X174 - 5386 bp late 1990’s - many additional microbial genomes sequenced including Archaea (Methanococcus jannaschii - 1996) and Eukaryotes (Saccharomyces cerevisiae - 1996)

Laboratory tools for studying whole genomes conventional techniques for analysing DNA are designed for the analysis of small regions of whole genomes such as individual genes or operons many of the techniques used to study whole genomes are conventional molecular biology techniques adapted to operate effectively with DNA in a much larger size range

Some tests : Pulsed Field Gel Electrophoresis Large insert cloning vectors – BAC’s and PAC’s Approaches to whole microbial genome sequencing Structural genomics Microarray hybridisation Random sequencing (shotgun) approach Genome Annotation

A typical Microbial project

Genome Annotation The process after sequencing has been completed. Use of many different tools required: Bioinformatics Databases Literature Sequence Experimental

Pipelines for the Annotation of Genomes – Web based

GLIMMER is a software for gene prediction and used by: BASYS- http://wishart.biology.ualberta.ca/basys/cgi/submit.pl JCVI (formerly TIGR)- http://www.tigr.org/ SABIA- http://www.sabia.lncc.br/

Example - Haemophilus influenzae first complete genome sequence of a free living organism (1995) important pathogen genome is around 1.83 megabases in size random sequencing was done for both small insert and large insert (lambda) libraries sequencing reactions performed by eight individuals using fourteen ABI 377 DNA sequencers per day over a three month period in total around 33000 sequencing reactions were performed on 20000 templates plasmid extraction performed in a 96 well format 11 mb of sequence was intially used to generate 140 contigs gaps were closed by lambda linking clones (23), peptide links (2), Southern analysis (37) and PCR (42)