, 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


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.


Sequencing MLSA ANI score Genome plasticity Pan-core plot 



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.


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

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13199_2016_401_MOESM2_ESM.doc (58 kb)
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13199_2016_401_MOESM3_ESM.doc (28 kb)
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  1. Armengol ,L, Pujana MA, Cheung J, Scherer SW, Estivill X (2003) Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum Mol Genet 12:2201–2208CrossRefPubMedGoogle Scholar
  2. Bajwa BS (2004) Molecular characterization of Frankia and Alder-Frankia symbiosis in Eastern India. Ph. D Thesis, NBU, SiliguriGoogle Scholar
  3. Benson DR, Silvester WB (1993) Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev 57:293PubMedPubMedCentralGoogle Scholar
  4. Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T (2013) antiSMASH 2.0–a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41:W204–W212. doi: 10.1093/nar/gkt449 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bose D, Sen A (2006) Isolation and heavy metal resistance pattern of Frankia from Casuarina equisetifolia nodules. Indian J Med Microbiol 46:9Google Scholar
  6. Carro L et al. (2013) Micromonospora is a normal occupant of actinorhizal nodules. J Biosci 38:685–693CrossRefPubMedGoogle Scholar
  7. Chen X, Zhang J (2013) Why are genes encoded on the lagging strand of the bacterial genome? GBE 5:2436–2439PubMedPubMedCentralGoogle Scholar
  8. Das S, Paul S, Dutta C (2006) Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei. J Mol Evol 62:645–658CrossRefPubMedGoogle Scholar
  9. De Mendoza A, Suga H, Ruiz-Trillo I (2010) Evolution of the MAGUK protein gene family in premetazoan lineages. BMC Evol Biol 10:93CrossRefPubMedPubMedCentralGoogle Scholar
  10. Di Marco A, Spalla C (1957) La produzione di cobalamine da fermentazione con una nuova specie di Nocardia: Nocardia rugosa. Giorn Microbiol 4:24–30Google Scholar
  11. Ghodhbane-Gtari F, Tisa LS (2014) Ecology and physiology of non-frankia actinobacteria from actinorhizal plants. In: Plasticity in plant-growth-promoting and phytopathogenic bacteria. Springer, New York, p 27–42Google Scholar
  12. Ghodhbane-Gtari F, Essoussi I, Chattaoui M, et al. (2010) Isolation and characterization of non-Frankia actinobacteria from root nodules of Alnus glutinosa, Casuarina glauca and Elaeagnus angustofolia. Symbiosis 50:51–57CrossRefGoogle Scholar
  13. Gnerre S et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS 108:1513–1518CrossRefPubMedGoogle Scholar
  14. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224CrossRefPubMedGoogle Scholar
  15. Hibbs DE, Cromack K Jr. (1990) Actinorhizal plants in Pacific Northwest forests. In: Schwintzer CR, Tjepkema JD (eds) The biology of frankia and actinorhizal plants. Academic Press, San Diego, p 343–363Google Scholar
  16. Hoagland DR, Arnon DI (1950) The water-culture method for growing plants without soil. Calif Agr Expt Sta Circ 347(2):32Google Scholar
  17. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi: 10.1186/1471-2105-11-119 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299–314Google Scholar
  19. Kim SB, Goodfellow M (1999) Reclassification of Amycolatopsis rugosa lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Evol Microbiol 49:507–512Google Scholar
  20. Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351CrossRefPubMedGoogle Scholar
  21. Kuhn K et al. (2004) A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 14:2347–2356CrossRefPubMedPubMedCentralGoogle Scholar
  22. Lalonde M, Calvert HE (1979) Production of Frankia hyphae and spores as an infective inoculant for Alnus species. Symbiotic Nitrogen Fixation in the Management of Temperate Forests 95:110Google Scholar
  23. Lechevalier MP, Prauser H, Labeda DP, Ruan JS (1986) Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Evol Microbiol 36:29–37Google Scholar
  24. Li K-B (2003) ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19:1585–1586CrossRefPubMedGoogle Scholar
  25. Li W-J, Xu P, Tang S-K, Xu L-H, Kroppenstedt RM, Stackebrandt E, Jiang C-L (2003) Prauserella halophila sp. nov. and Prauserella alba sp. nov., moderately halophilic actinomycetes from saline soil. Int J Syst Evol Microbiol 53:1545–1549CrossRefPubMedGoogle Scholar
  26. Li Y, Tang S-K, Chen Y-G, Wu J-Y, Zhi X-Y, Zhang Y-Q, Li W-J (2009) Prauserella salsuginis sp. nov., Prauserella flava sp. nov., Prauserella aidingensis sp. nov. and Prauserella sediminis sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 59:2923–2928CrossRefPubMedGoogle Scholar
  27. Liu N, Wang H, Liu M, Gu Q, Zheng W, Huang Y (2009) Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis. Int J Syst Evol Microbiol 59:254–258CrossRefPubMedGoogle Scholar
  28. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefPubMedPubMedCentralGoogle Scholar
  29. Maldonado LA, Quintana ET (2015) Unexpected properties of Micromonosporae from marine origin. Adv Microbiol 5:452–456CrossRefGoogle Scholar
  30. Markowitz VM et al. (2006) The integrated microbial genomes(IMG) system. Nucleic Acids Res 34:D344–D348. doi: 10.1093/Nar/Gkj024 CrossRefPubMedGoogle Scholar
  31. Markowitz VM et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122CrossRefPubMedGoogle Scholar
  32. Mavromatis K, Ivanova NN, Chen IMA, Szeto E, Markowitz VM, Kyrpides NC (2009) The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 1:63CrossRefPubMedPubMedCentralGoogle Scholar
  33. Medema MH et al. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. doi: 10.1093/Nar/Gkr466 CrossRefPubMedPubMedCentralGoogle Scholar
  34. Meier-Kolthoff JP, Auch AF, Klenk H-P, Goker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60CrossRefPubMedPubMedCentralGoogle Scholar
  35. Normand P, Fernandez MP (2008) Evolution and diversity of Frankia. In: Prokaryotic symbionts in plants. Springer Berlin Heidelberg, pp 103–125Google Scholar
  36. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7:455–457CrossRefPubMedGoogle Scholar
  37. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196. doi: 10.1093/nar/gkm864 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Roy A, Mukhopadhyay S, Sarkar I, Sen A (2015) Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium.World J Microbiol Biotechnol 31(6):959–981. doi: 10.1007/s11274-015-1850-1
  39. Schafer J, Martin K, Kamfer P (2010) Prauserella muralis sp. nov., from the indoor environment. Int J Syst Evol Microbiol 60:287–290CrossRefPubMedGoogle Scholar
  40. Sen et al. (2014) The phylogeny of actinobacteria revisited in the light of complete genomes, the orders frankiales and micrococcales should be split into coherent entities. proposal of frankiales ord. nov., geodermatophilales ord. nov., acidothermales ord. nov. and nakamurellales ord. nov. Int J Syst Evol Microbiol 64:3821–3832CrossRefPubMedGoogle Scholar
  41. Siguier P, Parochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–D36CrossRefPubMedGoogle Scholar
  42. Solanki P, Kothari V (2011) Halophilic actinomycetes: salt-loving filaments. Int J Life Sci Technol 4:7–13Google Scholar
  43. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690CrossRefPubMedGoogle Scholar
  44. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539CrossRefPubMedGoogle Scholar
  45. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  46. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36CrossRefPubMedPubMedCentralGoogle Scholar
  47. Thomas TD (2008) The role of activated charcoal in plant tissue culture. Biotechnol Adv 26:618–631CrossRefPubMedGoogle Scholar
  48. Touchon M, Rocha EPC (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 24:969–981CrossRefPubMedGoogle Scholar
  49. Trujillo ME, Kroppenstedt RM, Schumann P, Carro L, Martanez-Molina E (2006) Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia. Int J Syst Evol Microbiol 56:2381–2385CrossRefPubMedGoogle Scholar
  50. Valdes M, Parez N-O, Estrada-de Los Santos P, Caballero-Mellado J, Pe-Cabriales JJ, Normand P, Hirsch AM (2005) Non-frankia actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia fix nitrogen. Appl Environ Microbiol 71:460–466CrossRefPubMedPubMedCentralGoogle Scholar
  51. Vesth T, Lagesen K, Ãn A, Ussery D (2013) CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One 8:e60120CrossRefPubMedPubMedCentralGoogle Scholar
  52. Wall LG (2000) The actinorhizal symbiosis. J Plant Growth Regul 19:167–182PubMedGoogle Scholar
  53. Wang J et al. (2010) Prauserella marina sp. nov., isolated from ocean sediment of the South China Sea. Int J Syst Evol Microbiol 60:985–989CrossRefPubMedGoogle Scholar
  54. Wheeler CT, Miller IM (1990) Current and potential uses of actinorhizal plants in Europe. The Biology of Frankia and Actinorhizal Plants 365:389Google Scholar

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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