title: Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.
abstract: New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the sequencing data obtained compared with traditional quality filter approaches. Data preprocessing prior to the de novo assembly enabled the use of known methodologies in the next-generation sequencing data assembly. Moreover, manual curation was proved to be essential for ensuring a quality assembly, which was validated by comparative genomics with other species of the genus Corynebacterium. The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli.
authors.affiliation: Institute of Biological Sciences, Federal University Pará, Belém, Pará, Brazil.
authors.forename: Rommel Thiago Jucá
authors.initials: RT
authors.lastname: Ramos
authors.forename: Adriana Ribeiro
authors.initials: AR
authors.lastname: Carneiro
authors.forename: Siomar de Castro
authors.initials: Sde C
authors.lastname: Soares
authors.forename: Anderson Rodrigues
authors.initials: AR
authors.lastname: dos Santos
authors.forename: Sintia
authors.initials: S
authors.lastname: Almeida
authors.forename: Luis
authors.initials: L
authors.lastname: Guimarães
authors.forename: Flávia
authors.initials: F
authors.lastname: Figueira
authors.forename: Eudes
authors.initials: E
authors.lastname: Barbosa
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003354:Corynebacterium Infections / Q000382:microbiology / Q000662:veterinary; D016925:Corynebacterium pseudotuberculosis / Q000235:genetics* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis; D055664:Electrochemical Techniques / Q000295:instrumentation / Q000379:methods; D004867:Equipment Design; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006734:Horse Diseases / Q000382:microbiology; D006736:Horses; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods; D012984:Software
chemical_list: D004269:DNA, Bacterial