Symbiosis

, Volume 70, Issue 1–3, pp 49–58 | Cite as

Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India

  • Debadin Bose
  • Indrani Sarkar
  • Reha Labar
  • Rediet Oshone
  • Shimaa Ghazal
  • Krystalynne Morris
  • Feseha Abebe-Akele
  • W. Kelley Thomas
  • Louis S. Tisa
  • Arnab Sen
Article

Abstract

A novel actinomycete strain, assigned as Am3, was isolated from the root nodules of Alnus nepalensis at Mirik hills, India. Analysis of the 16s rRNA gene sequence placed this new strain within the genus Prauserella. The genome was sequenced by Illumina sequencing and resulting 5.33-Mbp high quality draft genome sequenced with a G + C content of 70.0 % and 4828 candidate protein-encoding genes. Phylogenetically, Prauserella clusters very close to Amycolatopsis and was previously placed under the genus Amycolatopsis. Our main focus was to reveal the genomic similarities and dissimilarities of the newly sequenced Prauserella sp. Am3 with the type strain, Prauserella rugosa DSM 43194 T, and to determine its relationship with Amycolatopsis, which is happened to be the closest genus of Prauserella. Taking an in silico approach, bioinformatic analysis revealed that the core genome of Amycolatopsis and Prauserella contained 1589 genes. The two Prauserella genomes shared approximately 4224 genes, and 237 and 245 unique genes were found in the P. rugosa and Prauserella sp. Am3 genomes, respectively. Analysis of various phylogenetic trees including a 16s rRNA gene tree, MLSA protein-based tree and concatenated core-genome-based tree, placed both Prauserella genomes together with Amycolatopsis halophila YIM 93233 as its closest neighbor. Blast Matrix analysis of the predicted proteomes revealed about 86 % homology between the two Prauserella genomes. Analysis of the strand variation property revealed the absence of replication-transcriptional selection. Overall, a high degree of similarity was found between the two Prauserella genomes and a high percentage of similarity occurred among the Prauserella genomes and Amycolatopsis halophila.

Keywords

Sequencing MLSA ANI score Genome plasticity Pan-core plot 

Notes

Acknowledgments

This work was supported by the USDA National Institute of Food and Agriculture Hatch 022821 (LST), and Department of Biotechnology, Govt. of West Bengal, India through grant no. 206/Bt (Estd.)/RD-22/2014 (AS). Authors acknowledge Department of Biotechnology, Govt. of India for the creation of Bioinformatics Facility at North Bengal University. IS acknowledges the receipt of BSR, UGC fellowship. Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2643. Sequencing was performed on an Illumina HiSeq2500 purchased with an NSF MRI Grant: DBI-1229361to WKThomas.

Compliance with ethical standards

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

Funding

This work is also partially supported by Department of Biotechnology, Govt. of West Bengal, India through grant no. 206/Bt(Estd.)/RD-22/2014. LST is supported in part by a USDA National Institute of Food and Agriculture Hatch 022821.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13199_2016_401_MOESM1_ESM.pdf (4 mb)
ESM 1 (PDF 4104 kb)
13199_2016_401_MOESM2_ESM.doc (58 kb)
ESM 2 (DOC 58 kb)
13199_2016_401_MOESM3_ESM.doc (28 kb)
ESM 3 (DOC 28 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Debadin Bose
    • 1
  • Indrani Sarkar
    • 1
  • Reha Labar
    • 1
  • Rediet Oshone
    • 2
  • Shimaa Ghazal
    • 2
  • Krystalynne Morris
    • 2
  • Feseha Abebe-Akele
    • 2
  • W. Kelley Thomas
    • 2
  • Louis S. Tisa
    • 2
  • Arnab Sen
    • 1
  1. 1.NBU Bioinformatics Facility, Department of BotanyUniversity of North BengalSiliguriIndia
  2. 2.Department of Molecular, Cellular & Biomedical SciencesUniversity of New HampshireDurhamUSA

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