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Draft genome of the Leptospira interrogans strains, Acegua, RCA, Prea, and Capivara, obtained from wildlife maintenance hosts and infected domestic animals

Abstract

In the present paper, we announce new draft genomes of four Leptospira interrogans strains named Acegua, RCA, Prea, and Capivara. These strains were isolated in the state of Rio Grande do Sul, Brazil, from cattle, dog, Brazilian guinea pig, and capybara, respectively.

Leptospirosis; genomics; neglected diseases; bioinformatics


The Leptospira genus comprises at least 22 different species, some of which, like Leptospira interrogans, Leptospira borgpetersenii, Leptospira santarosai, Leptospira noguchii, and Leptospira kirschneri, are pathogenic and may cause leptospirosis (Boonsilp et al. 2013Boonsilp S, Thaipadungpanit J, Amornchai P, Wuthiekanun V, Bailey MS, Holden MTG, Zhang C, Jiang X, Koizumi N, Taylor K, Galloway R, Hoffmaster AR, Craig S, Smythe LD, Hartskeerl RA, Day NP, Chantratita N, Feil EJ, Aanensen DM, Spratt BG, Peacock SJ 2013. A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species. PLoS Negl Trop Dis7: e1954.,Bourhy et al 2014Bourhy P, Collet L, Brisse S, Picardeau M 2014. Leptospira mayottensis sp. nov., a pathogenic species of the genusLeptospira isolated from humans. Int J Syst Evol Microbiol64: 4061-4067.). This neglected zoonosis is globally distributed and has become a reemerging public health problem in many countries, with stronger impact in tropical regions (Evangelista & Coburn 2010Evangelista KV, Coburn J 2010. Leptospira as an emerging pathogen: a review of its biology, pathogenesis, and host immune responses. Future Microbiol5: 1413-1425., Guerra 2013)Guerra MA 2013. Leptospirosis: public health perspectives.Biologicals41: 295-297.. Commonly found in rodents, leptospires may also infect and be hosted by different domestic and wildlife animals (Bharti et al. 2003)Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM, Lovett MA, Levett PN, Gilman RH, Willig MR, Gotuzzo E, Vinetz JM 2003. Leptospirosis: a zoonotic disease of global importance. Lancet Infect Dis3: 757-771.. This wide variety of reservoirs may play a key role in the maintenance and transmission of the disease (Levett 2001)Levett PN 2001. Leptospirosis. Clin Microbiol Rev14: 296-326.. Therefore, genome sequencing of isolates from different hosts potentially provides a starting point to towards understanding the ability of Leptospira spp to adapt to specific host and the basis of pathogen-host interaction.

In the present study, whole-genome sequencing was performed for the strains Acegua, isolated from a stillborn bovine foetus (Monte et al. 2015Monte LG, Ridieri KF, Jorge S, Oliveira NR, Hartwig DD, Amaral MG, Hartleben CP, Dellagostin OA 2015. Immunological and molecular characterization of Leptospira interrogans isolated from a bovine foetus.Comp Immunol Microbiol Infect Dis40: 41-45.), RCA, isolated from a domestic dog with clinical leptospirosis, Prea, isolated from Brazilian guinea pig (Cavia aperea) (Monte et al. 2013Monte LG, Jorge S, Xavier MA, Leal FMA, Amaral MG, Seixas FK, Dellagostin OA, Hartleben CP 2013. Molecular characterization of virulentLeptospira interrogans serogroup icterohaemorrhagiae isolated from Cavia aperea. Acta Trop126: 164-166.), and Capivara, isolated from capybara (Hydrochoerus hydrochaeris) (Jorge et al. 2012Jorge S, Monte LG, Coimbra MA, Albano AP, Hartwig DD, Lucas C, Seixas FK, Dellagostin OA, Hartleben CP 2012. Detection of virulence factors and molecular typing of pathogenic Leptospira from capybara (Hydrochaeris hydrochaeris). Curr Microbiol65: 461-464.).

The isolates were cultured in Ellinghausen-McCullough-Johnson-Harris (EMJH) medium supplemented with 10% Leptospira enrichment EMJH (Difco, USA), 200 μg/mL 5-fluorouracil, and 5% foetal calf serum in an incubator at 30ºC without agitation. DNA extraction was performed using the commercial Illustra Bacteria GenomicPrep Mini Spin kit (GE Healthcare, USA), following the manufacturer instructions.

The whole genome sequences were obtained using an Illumina MiSeq paired-end library for Acegua, an Illumina MiSeq paired-end library and an Ion Torrent PGM fragment library for RCA and Prea, and an Ion Torrent PGM fragment library for Capivara. The raw reads were filtered by quality using Fastx-Toolkit (hannonlab.cshl.edu/fastx_toolkit/) and the paired-end reads were trimmed using Trimmomatic (Bolger et al. 2014Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics30: 2114-2120.).

De novo assembly was performed using A5 (Tritt et al. 2012Tritt A, Eisen JA, Facciotti MT, Darling AE 2012. An integrated pipeline for de novo assembly of microbial genomes.PLoS ONE7: e42304.), SGA (Simpson & Durbin 2012Simpson JT, Durbin R 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res22: 549-556.), and Ray (Boisvert et al. 2010)Boisvert S, Laviolette F, Corbeil J 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol17: 1519-1533. for Acegua, A5, SGA, Ray, MIRA (chevreux.org/), Newbler (roche.com/), and SPAdes (Bankevich et al. 2012)Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin A V, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol19: 455-477. for RCA and Prea, and MIRA, Newbler, and SPAdes for Capivara. For each strain the de novo assemblies were merged using CISA (Lin & Liao 2013)Lin S-H, Liao Y-C 2013. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS ONE8: e60843. and evaluated using QUAST (Gurevich et al. 2013)Gurevich A, Saveliev V, Vyahhi N, Tesler G 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics29: 1072-1075.. Genome annotation was performed as previous described (Kremer et al. 2015)Kremer FS, Eslabão MR, Provisor M, Woloski RDS, Ramires OV, Moreno LZ, Moreno AM, Hamond C, Lilenbaum W, Dellagostin OA 2015. Draft genome sequences of Leptospira santarosai strains U160, U164, and U233, isolated from asymptomatic cattle. Genome Announc3: e00910-e00915. using Prodigal (Hyatt et al. 2010)Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics11: 119., NCBI-BLAST+ (Altschul et al. 1990Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol215: 403-410., Camacho et al. 2009)Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL 2009. BLAST+: architecture and applications. BMC Bioinformatics10: 421., Uniprot (Apweiler et al. 2004)Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh L-SL 2004. UniProt: the Universal Protein knowledgebase.Nucleic Acids Res32: D115-D119., HMMER (Eddy 2011)Eddy SR 2011. Accelerated profile HMM searches. PLoS Comput Biol7: e1002195., AntiFam (Eberhardt et al. 2012)Eberhardt RY, Haft DH, Punta M, Martin M, O’Donovan C, Bateman A 2012. AntiFam: a tool to help identify spurious ORFs in protein annotation.Database (Oxford)2012: bas003., tRNAscan-SE (Lowe & Eddy 1997)Lowe TM, Eddy SR 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res25: 955-964., RNAmmer (Lagesen et al. 2007)Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes.Nucleic Acids Res35: 3100-3108., INFERNAL (Nawrocki et al. 2009)Nawrocki EP, Kolbe DL, Eddy SR 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics25: 1335-1337., Aragorn (Laslett 2004)Laslett D 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res32: 11-16., and Rfam (Griffiths-Jones et al. 2003)Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR 2003. Rfam: an RNA family database. Nucleic Acids Res31: 439-441., and manually reviewed using Artemis (Rutherford et al. 2000)Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B 2000. Artemis: sequence visualization and annotation.Bioinformatics16: 944-945..

In silico multilocus sequence typing (MLST) was performed using BLASTn from the NCBI-BLAST+ and allele data from the Leptospira MLST scheme 1 (Boonsilp et al. 2013Boonsilp S, Thaipadungpanit J, Amornchai P, Wuthiekanun V, Bailey MS, Holden MTG, Zhang C, Jiang X, Koizumi N, Taylor K, Galloway R, Hoffmaster AR, Craig S, Smythe LD, Hartskeerl RA, Day NP, Chantratita N, Feil EJ, Aanensen DM, Spratt BG, Peacock SJ 2013. A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species. PLoS Negl Trop Dis7: e1954.), obtained from PubMLST repository (pubmlst.org/).

The results of the de novo assemblies are presented in Table I. The isolates were initially sequenced using only the Illumina platform, but the high fragmentation in the resulting assembly for Prea and RCA isolates (data not showed) motivated the use of a second next-generation sequencing technology to improve the original draft sequences. Although usually not required, the combination of data of two or more platforms in the sequencing of a given genome may result in a more accurate assembly, considering that each sequencing technology has it owns bias. The most common errors associated with Illumina data occurs on CG-poor and CG-rich regions, while IonTorrent, duo to its chemistry, has a high error-rate in homopolymeric regions. In fact, both characteristics are found inLeptospira genomes.

TABLE I
Summary of the assembly results

During genome annotation (Table II), by using our pipeline, in addition to the coding DNA sequences, we were also able to identify many noncoding feature in all four genomes, including not only transfer RNAs and ribosomal RNAs, but also transfer-messenger RNAs (tmRNAs), RNase P loci, and riboswitches. There is an increasing interest in the analysis of gene expression inLeptospira, especially during infection (Matsui et al. 2012Matsui M, Soupé M-E, Becam J, Goarant C 2012. Differential in vivo gene expression of major Leptospira proteins in resistant or susceptible animal models. Appl Environ Microbiol78: 6372-6376., Lehmann et al. 2013Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA 2013. Pathogenomic inference of virulence-associated genes in Leptospira interrogans. PLoS Negl Trop Dis7: e2468., Caimano et al. 2014Caimano MJ, Sivasankaran SK, Allard A, Hurley D, Hokamp K, Grassmann AA, Hinton JCD, Nally JE 2014. A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation byLeptospira interrogans serovar Copenhageni. PLoS Pathog10: e1004004., Eshghi et al. 2014Eshghi A, Becam J, Lambert A, Sismeiro O, Dillies M-A, Jagla B, Wunder EA, Ko AI, Coppee J-Y, Goarant C, Picardeau M 2014. A putative regulatory genetic locus modulates virulence in the pathogenLeptospira interrogans. Infect Immun82: 2542-2552.). Recent studies have already performed whole-transcriptome sequencing of L. interrogans and many noncoding features associated with gene expression regulation and transcriptional/translational processing were identified, including RNase P, tmRNAs, riboswitches, as well other families of noncoding RNA. Therefore, the identification of noncoding features in the annotation of newly sequenced genomes may allow a more accurate description of the resulting transcriptome.

TABLE II
Summary of the annotation results

The in silico MLST sequence types (ST) for the four isolates are presented in Table III. Previously identified by variable-number tandem-repeat asL. interrogans serogroup Australis serovar Muenchen (Monte et al. 2015Monte LG, Ridieri KF, Jorge S, Oliveira NR, Hartwig DD, Amaral MG, Hartleben CP, Dellagostin OA 2015. Immunological and molecular characterization of Leptospira interrogans isolated from a bovine foetus.Comp Immunol Microbiol Infect Dis40: 41-45.), the Acegua isolate was a match for ST24 that contains two L. interrogans serogroup Australis isolates, while the Capivara isolate was identified as ST17 that includes nine L. interrogans serogroup Icterohaemorrhagiae isolates (5 belonging to serovar Copenhageni and 2 to serovar Icterohaemorrhagiae). Preliminary analysis revealed that the pfkBlocus was absent in the draft assemblies of RCA and Prea. To investigate this fact, the raw reads from these isolates were aligned using BLASTn against a reference set of pfkB alleles obtained from the PubMLST repository. The BLAST XML output was analysed by a Python script to identify reads that correspond to this locus using an identity threshold of 95%. The selected reads were saved in FASTQ format and filtered by quality using a minimum Phred score of 20 in at least 95% of the bases. After filtering, 83 reads remained in the Prea set, and 90 in the RCA set, corresponding to mean coverages of about 18 and 20-fold, respectively. Therefore, the absence of this locus in both draft genomes was a result of an assembly artifact. For each genome, the reads that aligned to the pfkB database were assembled using CAP3 (Huang & Madan 1999Huang X, Madan A 1999. CAP3: A DNA sequence assembly program.Genome Res9: 868-877.) and the resulting contigs were aligned against the same database to identify the corresponding alleles in the MLST scheme 1, that are showed in Table III.

TABLE III
Sequence types (ST) profiles of the Acegua, RCA, Prea, and Capivara strains based on the Leptospira multilocus sequence typing scheme 1

The Leptospira genus comprises more than 300 serovars and pathogenic species were already reported in a wide variety of animal hosts. However, from the 233 genome sequences indexed in BioProject database and available at GenBank with host information, the major part (166) was obtained from human samples (ncbi.nlm.nih.gov/bioproject/). The sequencing of isolates obtained from wildlife animals, like C. aperea and H. hydrochaeris, both rodents and natural reservoirs, provide data for future pangenome and pathogenome analysis intending to understand the factors that guide the pathogen-host interactions. Additionally, the isolate Acegua, obtained from a bovine stillborn, also represents an interesting source of information about these interactions, since abortion induced by leptospirosis in cattle is usually associated to the serovar Hardjo of the speciesL. interrogans and L. borgpetersenii, not to Muenchen, although this serovar has been associated to abortions in pigs (Ellis et al. 1986Ellis WA, McParland PJ, Bryson DG, Thiermann AB, Montgomery J 1986. Isolation of leptospires from the genital tract and kidneys of aborted sows.Vet Rec118: 294-295.).

Finally, the analysis of these isolates also provide new insights into the serogroups circulating in the south of Brazil, suggesting that while L. interrogans serogroup Icterohaemorrhagiae serovars Icterohaemorrhagiae and Copenhageni are present, they are not the only ones. Based on the MLST profiles, serovars belonging to serogroup Australis are also circulating among wild and domestic animals, and the comparative analysis of genomic data may be applied to trace their distribution and evolution. Furthermore, the availability of these new genome sequences from four L. interrogans strains, isolated from diverse hosts, will provide useful data towards understanding the molecular diversity and pathogenesis of these new strains.

Nucleotide sequence accessions - These Whole Genome Shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accessions LCZF00000000 for Acegua, LJBP00000000 for RCA, LJBO00000000 for Prea, and LJBQ00000000 for Capivara. The versions described in this paper are LCZF01000000, LJBP01000000, LJBO01000000, and LJBQ01000000, respectively.

REFERENCES

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol215: 403-410.
  • Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh L-SL 2004. UniProt: the Universal Protein knowledgebase.Nucleic Acids Res32: D115-D119.
  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin A V, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol19: 455-477.
  • Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM, Lovett MA, Levett PN, Gilman RH, Willig MR, Gotuzzo E, Vinetz JM 2003. Leptospirosis: a zoonotic disease of global importance. Lancet Infect Dis3: 757-771.
  • Boisvert S, Laviolette F, Corbeil J 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol17: 1519-1533.
  • Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics30: 2114-2120.
  • Boonsilp S, Thaipadungpanit J, Amornchai P, Wuthiekanun V, Bailey MS, Holden MTG, Zhang C, Jiang X, Koizumi N, Taylor K, Galloway R, Hoffmaster AR, Craig S, Smythe LD, Hartskeerl RA, Day NP, Chantratita N, Feil EJ, Aanensen DM, Spratt BG, Peacock SJ 2013. A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species. PLoS Negl Trop Dis7: e1954.
  • Bourhy P, Collet L, Brisse S, Picardeau M 2014. Leptospira mayottensis sp. nov., a pathogenic species of the genusLeptospira isolated from humans. Int J Syst Evol Microbiol64: 4061-4067.
  • Caimano MJ, Sivasankaran SK, Allard A, Hurley D, Hokamp K, Grassmann AA, Hinton JCD, Nally JE 2014. A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation byLeptospira interrogans serovar Copenhageni. PLoS Pathog10: e1004004.
  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL 2009. BLAST+: architecture and applications. BMC Bioinformatics10: 421.
  • Eberhardt RY, Haft DH, Punta M, Martin M, O’Donovan C, Bateman A 2012. AntiFam: a tool to help identify spurious ORFs in protein annotation.Database (Oxford)2012: bas003.
  • Eddy SR 2011. Accelerated profile HMM searches. PLoS Comput Biol7: e1002195.
  • Ellis WA, McParland PJ, Bryson DG, Thiermann AB, Montgomery J 1986. Isolation of leptospires from the genital tract and kidneys of aborted sows.Vet Rec118: 294-295.
  • Eshghi A, Becam J, Lambert A, Sismeiro O, Dillies M-A, Jagla B, Wunder EA, Ko AI, Coppee J-Y, Goarant C, Picardeau M 2014. A putative regulatory genetic locus modulates virulence in the pathogenLeptospira interrogans Infect Immun82: 2542-2552.
  • Evangelista KV, Coburn J 2010. Leptospira as an emerging pathogen: a review of its biology, pathogenesis, and host immune responses. Future Microbiol5: 1413-1425.
  • Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR 2003. Rfam: an RNA family database. Nucleic Acids Res31: 439-441.
  • Guerra MA 2013. Leptospirosis: public health perspectives.Biologicals41: 295-297.
  • Gurevich A, Saveliev V, Vyahhi N, Tesler G 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics29: 1072-1075.
  • Huang X, Madan A 1999. CAP3: A DNA sequence assembly program.Genome Res9: 868-877.
  • Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics11: 119.
  • Jorge S, Monte LG, Coimbra MA, Albano AP, Hartwig DD, Lucas C, Seixas FK, Dellagostin OA, Hartleben CP 2012. Detection of virulence factors and molecular typing of pathogenic Leptospira from capybara (Hydrochaeris hydrochaeris). Curr Microbiol65: 461-464.
  • Kremer FS, Eslabão MR, Provisor M, Woloski RDS, Ramires OV, Moreno LZ, Moreno AM, Hamond C, Lilenbaum W, Dellagostin OA 2015. Draft genome sequences of Leptospira santarosai strains U160, U164, and U233, isolated from asymptomatic cattle. Genome Announc3: e00910-e00915.
  • Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes.Nucleic Acids Res35: 3100-3108.
  • Laslett D 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res32: 11-16.
  • Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA 2013. Pathogenomic inference of virulence-associated genes in Leptospira interrogans PLoS Negl Trop Dis7: e2468.
  • Levett PN 2001. Leptospirosis. Clin Microbiol Rev14: 296-326.
  • Lin S-H, Liao Y-C 2013. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS ONE8: e60843.
  • Lowe TM, Eddy SR 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res25: 955-964.
  • Matsui M, Soupé M-E, Becam J, Goarant C 2012. Differential in vivo gene expression of major Leptospira proteins in resistant or susceptible animal models. Appl Environ Microbiol78: 6372-6376.
  • Monte LG, Jorge S, Xavier MA, Leal FMA, Amaral MG, Seixas FK, Dellagostin OA, Hartleben CP 2013. Molecular characterization of virulentLeptospira interrogans serogroup icterohaemorrhagiae isolated from Cavia aperea Acta Trop126: 164-166.
  • Monte LG, Ridieri KF, Jorge S, Oliveira NR, Hartwig DD, Amaral MG, Hartleben CP, Dellagostin OA 2015. Immunological and molecular characterization of Leptospira interrogans isolated from a bovine foetus.Comp Immunol Microbiol Infect Dis40: 41-45.
  • Nawrocki EP, Kolbe DL, Eddy SR 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics25: 1335-1337.
  • Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B 2000. Artemis: sequence visualization and annotation.Bioinformatics16: 944-945.
  • Simpson JT, Durbin R 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res22: 549-556.
  • Tritt A, Eisen JA, Facciotti MT, Darling AE 2012. An integrated pipeline for de novo assembly of microbial genomes.PLoS ONE7: e42304.
  • Financial support: CNPq, CAPES, FAPERGS, FAPESP (2011/18290-0, 2013/17136-2)

Publication Dates

  • Publication in this collection
    Apr 2016

History

  • Received
    12 Jan 2016
  • Accepted
    3 Mar 2016
Instituto Oswaldo Cruz, Ministério da Saúde Av. Brasil, 4365 - Pavilhão Mourisco, Manguinhos, 21040-900 Rio de Janeiro RJ Brazil, Tel.: (55 21) 2562-1222, Fax: (55 21) 2562 1220 - Rio de Janeiro - RJ - Brazil
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