Ecogenomics and Its main Objectives

The study of structure and function of a genome in order to understand its relationship between the organism and biotic and abiotic factors of the environment is called ecogenomics. The main objectives of ecogenomics are as follows:

1. To investigate the evolution pattern of an organism with the help of DNA sequences.

2. To discover and explore uncultivable microorganisms with the help of metagenomic techniques.

3. To study the relationship between a species and effect of environmental factors on the species at a molecular level utilizing DNA microarray.

4. To study the effect of genetic and epigenetic variation on evolutionary change due to stress.

5. To study the relationship between different species and gene-environment-function with the help of comparative genomics.

6.  Assessment of region specific biodiversity with the help of DNA microarrays and find the difference between impacted and control regions.

There are several projects going on in order to get more insight into the composition and working of microbes and other soil organisms at a genetic level. For example, a new species of thermophilic bacteria was discovered in order to understand the life sustainable system in the soil by ecogenomics. Samples at a depth of about 8,000 ft below the surface from a gold mine were collected for genome analysis in in South Africa, Witwatersrand Basin. The DNA was extracted from fracture water. Analysis of 16s rDNA in the sample showed that a sulfate reducer and a methylotroph with some thermophilic microbes were present in high quantity. In the thermophiles obtained, there was a dominant Desulfotomaculum like organism discovered which supposedly represented a new species and new family of thermophiles. This organism has several differences from other thermophiles and sulfate reducers in terms of biosustainability in deep subsurface environments so are considered to be a completely new species.

Ecogenomics not only has application in general and pure science but it is also used to understand the function of microbial communities in disease processes which cannot be understood by traditional culture based methods like metagenomics.

While researching the in situ communities like the host system, ecogenomics allows studying the interaction of a pathogen with other microorganisms. This may help to keep a check on the pathogen if the interaction is antagonistic.

With the help of ecogenomics, extensive amounts of genetic information can be analyzed and generated. It can used to explore several factors such as ecological systems which enable the scientists to analyze thoroughly and make more reliable and specific decisions for ecosystem viability.

Ecogenomics can be utilized to determine several aspects altogether as compared to other techniques such as metagenomics. Ecogenomics may investigate factors such as interactions of food web in aquatic environments, spraying effects of fertilizer, ecological effects of different pesticide and land management and functioning in terms of sediment and soil biodiversity. Whereas traditional techniques can analyze limited factors at a time, for example metagenomics studies only the genetics of environmental samples. 

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Genome Sequencing Strategy

Here we have discussed a genome sequencing strategy which is commonly adapted in labs.

The steps in the complete genome sequencing will generate the cDNA sequences that can be used to develop BACs and cDNA microarrays. But since there limited genome data of the organism available, the sequencing will be carried out in two distinct stages.

 

Stage I:

In this stage, the cDNA library of the organism will be generated. The database of novel EST’s from the most diverse EST library would be prepared that can be used for gene annotation, cloning and development of microarray’s etc. The EST’s will expand the understanding of types of genes expressed in the organism . The genome size of the organism will be estimated by comparing the reassociation rate. The genome size will provide a significant information by which we aim to generate BAC genomic DNA library that will inform about GC content of the genome, repetitive sequences and level of polymorphism in the genome.

Stage II:

In this stage, whole genome random shotgun sequencing is proposed for the complete genome sequencing of the organism. This method utilizes comparative genomics protein coding and regulatory regions on the genome. The sequence-tagged BAC clones are mapped to the polytene chromosomes so as assembled scaffolds are directly localized in the genome of the organism  with specific orientations. We aim to produce a draft genome with the knowledge of genomic organization, to carry out the comparative genome analysis and the complete finishing of the genome is done. The finished genome is released to a public domain after getting approval by several committees.