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Antonie van Leeuwenhoek

, Volume 112, Issue 1, pp 101–107 | Cite as

A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria

  • Indrani Sarkar
  • Maher Gtari
  • Louis S. Tisa
  • Arnab SenEmail author
Original Paper
  • 78 Downloads

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.

Keywords

Protein functional domains Binary data Phylogenetic tree Biological network 

Notes

Authors contribution

AS conceived the idea. AS and IS designed the study, performed research and analysed data. AS, IS, LT and MG wrote the paper.

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

10482_2018_1154_MOESM1_ESM.docx (17 kb)
ST1: List of all the 100 Actinobacteria considered for this study (DOCX 16 kb)
10482_2018_1154_MOESM2_ESM.xlsx (1.5 mb)
ESM1: Total pan- (sheet1) and core (sheet2) domains among selected actinobacteria and biological enrichment analysis of core domains (sheet3) (XLSX 1536 kb)
10482_2018_1154_MOESM3_ESM.xlsx (54 kb)
ESM2: (a) List of shared domains among thermal niche adapting Acidothermus cellulolyticus and Acidimicrobium ferroxidens (XLSX 54 kb)
10482_2018_1154_MOESM4_ESM.pdf (13.7 mb)
ESM2: (b) biological network analysis of shared domains among thermal niche adapting Acidothermus cellulolyticus and Acidimicrobium ferroxidens (PDF 13985 kb)
10482_2018_1154_MOESM5_ESM.xlsx (70 kb)
ESM3: (a) List of shared domains among Kineococcus radiotolerans, Jonesia denitrificans and Sanguibacter keddieii (XLSX 69 kb)
10482_2018_1154_MOESM6_ESM.pdf (7.5 mb)
ESM3: (b) biological network analysis of shared domains among Kineococcus radiotolerans, Jonesia denitrificans and Sanguibacter keddieii (PDF 7658 kb)
10482_2018_1154_MOESM7_ESM.xlsx (58 kb)
ESM4: (a) List of shared domains among Kytococcus sedentarius and Micrococcus luteus (XLSX 57 kb)
10482_2018_1154_MOESM8_ESM.pdf (5.8 mb)
ESM4: (b) biological network analysis of shared domains among Kytococcus sedentarius and Micrococcus luteus (PDF 5909 kb)
10482_2018_1154_MOESM9_ESM.xlsx (66 kb)
ESM5: (a) List of shared domains among Kribbella flavida and Micromonosporales (XLSX 65 kb)
10482_2018_1154_MOESM10_ESM.pdf (6.4 mb)
ESM5: (b) biological network analysis of shared domains among Kribbella flavida and Micromonosporales (PDF 6525 kb)
10482_2018_1154_MOESM11_ESM.xlsx (81 kb)
ESM6: (a) List of shared domains among Stackebrandtia nassauensis and Saccharopolyspora erythraea (XLSX 81 kb)
10482_2018_1154_MOESM12_ESM.pdf (6 mb)
ESM6: (b) biological network analysis of shared domains among Stackebrandtia nassauensis and Saccharopolyspora erythraea (PDF 6187 kb)
10482_2018_1154_MOESM13_ESM.xlsx (63 kb)
ESM7: (a) List of shared domains among Intrasporangium calvum and Nocardioides dokdonensis (XLSX 63 kb)
10482_2018_1154_MOESM14_ESM.pdf (5.9 mb)
ESM7: (b) biological network analysis of shared domains among Intrasporangium calvum and Nocardioides dokdonensis (PDF 6053 kb)
10482_2018_1154_MOESM15_ESM.xlsx (8 kb)
ESM8: (a) Enrichment analysis of shared domains between Conexibacter woesei and Rubrobacter xylanophilus (XLSX 8 kb)
10482_2018_1154_MOESM16_ESM.pdf (778 kb)
ESM8: (b) biological network of shared domains between Conexibacter woesei and Rubrobacter xylanophilus (PDF 778 kb)

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Indrani Sarkar
    • 1
  • Maher Gtari
    • 2
  • Louis S. Tisa
    • 3
  • Arnab Sen
    • 1
    Email author
  1. 1.NBU Bioinformatics Facility, Department of BotanyUniversity of North BengalSiliguriIndia
  2. 2.Institut National des Sciences Appliquées et de TechnologieUniversité CarthageTunis CedexTunisia
  3. 3.Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamUSA

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