A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria
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Protein functional domains are semi-autonomous parts of proteins capable of functioning independently. One protein may contain several domains and one domain may be present in different protein sequences. Thus, protein domains represent the niche specific adaptive nature of an organism. We hypothesized that the presence and absence of protein domains in an organism could be used to make a phylogenetic tree, which may better depict the biotope (niche). Here, we selected 100 actinobacteria and built a phylogenetic tree depending upon the presence and absence of protein domains. Strains of different genera from the same niche were found to cluster together suggesting niche specific domain acquisition among selected strains. Thus, the domain based phylogeny clustered the selected actinobacteria mainly according to their niche rather than their taxonomic classification.
KeywordsProtein functional domains Binary data Phylogenetic tree Biological network
AS conceived the idea. AS and IS designed the study, performed research and analysed data. AS, IS, LT and MG wrote the paper.
IS acknowledges UGC-BSR senior research fellowship, Govt, of India. AS is thankful to DBT, Government of India, for funding Bioinformatics Facility at University of North Bengal.AS also acknowledges DST, Government of India for sanctioning the Indo-Tunis joint research project (DST/INT/TUINISIA/P-05/2017).LST acknowledges the USDA National Institute of Food and Agriculture Hatch 022821.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
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