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Homology modeling in combination of phylogenetic assortment, a new approach to resolve the phylogeny of selected heterocystous cyanobacteria based on phycocyanin encoding cpcBA-IGS locus

Abstract

The present communication deals with phylogenetic assessment of phycocyanin coding genes, based on their 3-D structures which is still in its infancy. Homology modeling of cpcA and cpcB in conjunction with molecular phylogenetics for 12 strains belonging to the heterocystous cyanobacteria has been performed with an aim to resolve the ambiguities in their phylogenetic positions. 3D structure has been deduced using Discovery studio while CHIMERA, PEROMALS3D and SALIGN tools have been used for studying the structure based diversity of cpcA and cpcB genes respectively. MEME suite has been further used for motif analysis. Calothrix brevissima Ind9 was the most divergent strain. Nostoc and Anabaena were found to be intermixed at structural level also. The phylogeny suggested monophyletic origin of the heterocystous clade. Conserved Signature Indels provides novel means of identification and also supported monophyletic origin of heterocystous cyanobacteria. At the structure level the secondary elements are more conserved. Overall data obtained through the 3D structure based phylogeny affirmed close association and similar origin of the two subsections. This approach provides better resolution and must be used along with molecular phylogenetics for better identification of cyanobacteria.

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Acknowledgements

Authors are thankful to the Head, Department of Botany, Banaras Hindu University, Varanasi, India. Ekta Shukla is also thankful to the CSIR, New Delhi, India for the financial support in the form of SRF. Prof. Ashok Kumar and Prof. S.M. Singh, and Centre of Bionformatics, School of Biotechnology, Banaras Hindu University are greatly acknowledged for providing facilities.

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ES and AKM designed and performed the research. ES, PS and VKS analyzed the data. AKM and SSS critically reviewed the paper.

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Correspondence to Arun Kumar Mishra.

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Supplementary Information

Below is the link to the electronic supplementary material.

42535_2021_207_MOESM1_ESM.tif

Supplementary file1 Multiple sequence alignment (CLC sequence viewer7) of cpcBA-IGS locus of 54 heterocystous cyanobacterial strains. (TIF 3687 KB)

Supplementary file2 Ramchandran Plot analysis of the 3D modeled structures of cpcA and cpcB gene (TIF 3843 KB)

42535_2021_207_MOESM3_ESM.doc

Supplementary file3 (a) and (b) Superimposition of target and template files of cpcA and cpcB gene by Superimpose tool (DOC 3548 KB)

Supplementary file4 (DOC 1203 KB)

Supplementary file5 (DOC 32 KB)

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Shukla, E., Singh, P., Singh, V.K. et al. Homology modeling in combination of phylogenetic assortment, a new approach to resolve the phylogeny of selected heterocystous cyanobacteria based on phycocyanin encoding cpcBA-IGS locus. Vegetos 34, 339–354 (2021). https://doi.org/10.1007/s42535-021-00207-z

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Keywords

  • cpcA and cpcB genes
  • CpcBA-IGS locus
  • Conserved signature indels
  • 3-D homology modeling
  • Phylogeny