finding environment specific genes

Question

[glady]

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.

[WouterDeCoster]

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?

Answer 1

[natasha.sernova]

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

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC515249/

[WouterDeCoster]

Which of these links discusses how to detect a gene unique for a specific environment?

[glady]

Thank you for your suggestion.