publication . Other literature type . Article . 2017

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas.

Vyacheslav Yurchenko; Pavel Flegontov; Alexei Yu. Kostygov;
Open Access
  • Published: 01 Oct 2017
  • Publisher: Frontiers Media SA
Abstract
We have sequenced, annotated and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts' genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. Pandoraea novymonadis lacks mobile elements, has a strikingly low number of pseudogenes and almost all genes are single copied. This suggests that it already passed the intensive period of host adaptation, which still can be observed in the...
Subjects
Medical Subject Headings: fungibiochemical phenomena, metabolism, and nutrition
free text keywords: bacterial endosymbiont, Pandoraea, phylogenomics, metabolism, Trypanosomatidae, Microbiology, QR1-502, Original Research, Microbiology (medical)
82 references, page 1 of 6

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Alves J. M.Klein C. C.da Silva F. M.Costa-Martins A. G.Serrano M. G.Buck G. A. (2013a). Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. BMC Evol. Biol. 13:190 10.1186/1471-2148-13-190 [OpenAIRE] [DOI]

Alves J. M.Serrano M. G.Maia da Silva F.Voegtly L. J.Matveyev A. V. (2013b). Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. Genome Biol. Evol. 5 338–350. 10.1093/gbe/evt012 23345457 [OpenAIRE] [PubMed] [DOI]

Alves J. M.Voegtly L.Matveyev A. V.Lara A. M.da Silva F. M.Serrano M. G. (2011). Identification and phylogenetic analysis of heme synthesis genes in trypanosomatids and their bacterial endosymbionts. PLOS ONE 6:e23518 10.1371/journal.pone.0023518 [OpenAIRE] [DOI]

Alves J. M. (2017). “Amino acid biosynthesis in endosymbiont-harbouring Trypanosomatidae,” in The Handbook of Microbial Metabolism of Amino Acids ed. D’Mello J. P. F. (Oxfordshire: CAB International) 371–383.

Anandham R.Indiragandhi P.Kwon S. W.Sa T. M.Jeon C. O.Kim Y. K. (2010). Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int. J. Syst. Evol. Microbiol. 60(Pt 1) 21–26. 10.1099/ijs.0.012823-0 19643869 [OpenAIRE] [PubMed] [DOI]

Arndt D.Grant J. R.Marcu A.Sajed T.Pon A.Liang Y. (2016). PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44 W16–W21. 10.1093/nar/gkw387 27141966 [OpenAIRE] [PubMed] [DOI]

Arpigny J. L.Jaeger K. E. (1999). Bacterial lipolytic enzymes: classification and properties. Biochem. J. 343(Pt 1) 177–183. 10.1042/bj3430177 10493927 [OpenAIRE] [PubMed] [DOI]

Bankevich A.Nurk S.Antipov D.Gurevich A. A.Dvorkin M.Kulikov A. S. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19 455–477. 10.1089/cmb.2012.0021 22506599 [OpenAIRE] [PubMed] [DOI]

Barry A.Bryskier A.Traczewski M.Brown S. (2004). Preparation of stock solutions of macrolide and ketolide compounds for antimicrobial susceptibility tests. Clin. Microbiol. Infect. 10 78–83. 10.1111/j.1469-0691.2004.00759.x 14706092 [OpenAIRE] [PubMed] [DOI]

Boscaro V.Felletti M.Vannini C.Ackerman M. S.Chain P. S.Malfatti S. (2013). Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proc. Natl. Acad. Sci. U.S.A. 110 18590–18595. 10.1073/pnas.1316687110 24167248 [OpenAIRE] [PubMed] [DOI]

Boscaro V.Kolisko M.Felletti M.Vannini C.Lynn D. H.Keeling P. J. (2017). Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat. Ecol. Evol. 1 1160–1167. 10.1038/s41559-017-0237-0 [OpenAIRE] [DOI]

Botzman M.Margalit H. (2011). Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biol. 12:R109 10.1186/gb-2011-12-10-r109 [OpenAIRE] [DOI]

Burke G. R.Moran N. A. (2011). Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biol. Evol. 3 195–208. 10.1093/gbe/evr002 21266540 [OpenAIRE] [PubMed] [DOI]

Camacho C.Coulouris G.Avagyan V.Ma N.Papadopoulos J.Bealer K. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421 10.1186/1471-2105-10-421 [OpenAIRE] [DOI]

82 references, page 1 of 6
Abstract
We have sequenced, annotated and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts' genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. Pandoraea novymonadis lacks mobile elements, has a strikingly low number of pseudogenes and almost all genes are single copied. This suggests that it already passed the intensive period of host adaptation, which still can be observed in the...
Subjects
Medical Subject Headings: fungibiochemical phenomena, metabolism, and nutrition
free text keywords: bacterial endosymbiont, Pandoraea, phylogenomics, metabolism, Trypanosomatidae, Microbiology, QR1-502, Original Research, Microbiology (medical)
82 references, page 1 of 6

Akhter S.Aziz R. K.Edwards R. A. (2012). PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res. 40 e126 10.1093/nar/gks406 [OpenAIRE] [DOI]

Alves J. M.Klein C. C.da Silva F. M.Costa-Martins A. G.Serrano M. G.Buck G. A. (2013a). Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. BMC Evol. Biol. 13:190 10.1186/1471-2148-13-190 [OpenAIRE] [DOI]

Alves J. M.Serrano M. G.Maia da Silva F.Voegtly L. J.Matveyev A. V. (2013b). Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. Genome Biol. Evol. 5 338–350. 10.1093/gbe/evt012 23345457 [OpenAIRE] [PubMed] [DOI]

Alves J. M.Voegtly L.Matveyev A. V.Lara A. M.da Silva F. M.Serrano M. G. (2011). Identification and phylogenetic analysis of heme synthesis genes in trypanosomatids and their bacterial endosymbionts. PLOS ONE 6:e23518 10.1371/journal.pone.0023518 [OpenAIRE] [DOI]

Alves J. M. (2017). “Amino acid biosynthesis in endosymbiont-harbouring Trypanosomatidae,” in The Handbook of Microbial Metabolism of Amino Acids ed. D’Mello J. P. F. (Oxfordshire: CAB International) 371–383.

Anandham R.Indiragandhi P.Kwon S. W.Sa T. M.Jeon C. O.Kim Y. K. (2010). Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). Int. J. Syst. Evol. Microbiol. 60(Pt 1) 21–26. 10.1099/ijs.0.012823-0 19643869 [OpenAIRE] [PubMed] [DOI]

Arndt D.Grant J. R.Marcu A.Sajed T.Pon A.Liang Y. (2016). PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44 W16–W21. 10.1093/nar/gkw387 27141966 [OpenAIRE] [PubMed] [DOI]

Arpigny J. L.Jaeger K. E. (1999). Bacterial lipolytic enzymes: classification and properties. Biochem. J. 343(Pt 1) 177–183. 10.1042/bj3430177 10493927 [OpenAIRE] [PubMed] [DOI]

Bankevich A.Nurk S.Antipov D.Gurevich A. A.Dvorkin M.Kulikov A. S. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19 455–477. 10.1089/cmb.2012.0021 22506599 [OpenAIRE] [PubMed] [DOI]

Barry A.Bryskier A.Traczewski M.Brown S. (2004). Preparation of stock solutions of macrolide and ketolide compounds for antimicrobial susceptibility tests. Clin. Microbiol. Infect. 10 78–83. 10.1111/j.1469-0691.2004.00759.x 14706092 [OpenAIRE] [PubMed] [DOI]

Boscaro V.Felletti M.Vannini C.Ackerman M. S.Chain P. S.Malfatti S. (2013). Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proc. Natl. Acad. Sci. U.S.A. 110 18590–18595. 10.1073/pnas.1316687110 24167248 [OpenAIRE] [PubMed] [DOI]

Boscaro V.Kolisko M.Felletti M.Vannini C.Lynn D. H.Keeling P. J. (2017). Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat. Ecol. Evol. 1 1160–1167. 10.1038/s41559-017-0237-0 [OpenAIRE] [DOI]

Botzman M.Margalit H. (2011). Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biol. 12:R109 10.1186/gb-2011-12-10-r109 [OpenAIRE] [DOI]

Burke G. R.Moran N. A. (2011). Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biol. Evol. 3 195–208. 10.1093/gbe/evr002 21266540 [OpenAIRE] [PubMed] [DOI]

Camacho C.Coulouris G.Avagyan V.Ma N.Papadopoulos J.Bealer K. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421 10.1186/1471-2105-10-421 [OpenAIRE] [DOI]

82 references, page 1 of 6
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