I want to find environment specific genes in a genome. so that I can differentiate two genomes of same species coming from different ecological niche.
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Look at this post. It's 3 years old but it may be helpful.
Methods For Investigating Gene-Environment Interactions?
Also see the following articles:
A framework for incorporating evolutionary genomics into biodiversity conservation and management, from 2015
https://climatechangeresponses.biomedcentral.com/articles/10.1186/s40665-014-0009-x
Some others are much older bacterial articles
Detecting genetic responses to environmental change
http://sci-hub.cc/10.1038/nrg2339#
Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168647/
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
Which of these links discusses how to detect a gene unique for a specific environment?
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What type of data (and how much samples) do you have available? Are you really looking for a whole gene, or would a few variants (SNPs) also be sufficient to differentiate the organisms?