Abstract
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.
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Funding
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.
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AS conceived the idea. AS and IS designed the study, performed research and analysed data. AS, IS, LT and MG wrote the paper.
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ESM1: Total pan- (sheet1) and core (sheet2) domains among selected actinobacteria and biological enrichment analysis of core domains (sheet3) (XLSX 1536 kb)
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ESM2: (a) List of shared domains among thermal niche adapting Acidothermus cellulolyticus and Acidimicrobium ferroxidens (XLSX 54 kb)
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ESM2: (b) biological network analysis of shared domains among thermal niche adapting Acidothermus cellulolyticus and Acidimicrobium ferroxidens (PDF 13985 kb)
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ESM3: (a) List of shared domains among Kineococcus radiotolerans, Jonesia denitrificans and Sanguibacter keddieii (XLSX 69 kb)
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ESM3: (b) biological network analysis of shared domains among Kineococcus radiotolerans, Jonesia denitrificans and Sanguibacter keddieii (PDF 7658 kb)
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ESM4: (b) biological network analysis of shared domains among Kytococcus sedentarius and Micrococcus luteus (PDF 5909 kb)
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ESM6: (b) biological network analysis of shared domains among Stackebrandtia nassauensis and Saccharopolyspora erythraea (PDF 6187 kb)
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ESM7: (b) biological network analysis of shared domains among Intrasporangium calvum and Nocardioides dokdonensis (PDF 6053 kb)
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Sarkar, I., Gtari, M., Tisa, L.S. et al. A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria. Antonie van Leeuwenhoek 112, 101–107 (2019). https://doi.org/10.1007/s10482-018-1154-1
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DOI: https://doi.org/10.1007/s10482-018-1154-1