title: PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity.
abstract: We have sequenced a Burkholderia genome that contains multiple replicons and large repetitive elements that would make it inherently difficult to assemble by short read sequencing technologies. We illustrate how the integrated long read correction algorithms implemented through the PacBio Single Molecule Real-Time (SMRT) sequencing technology successfully provided a de novo assembly that is a reasonable estimate of both the gene content and genome organization without making any further modifications. This assembly is comparable to related organisms assembled by more labour intensive methods. Our assembled genome revealed regions of genome plasticity for further investigation, one of which harbours a chlorocatechol degradative operon highly homologous to those previously identified on globally ubiquitous plasmids. In an ideal world, this assembly would still require experimental validation to confirm gene order and copy number of repeated elements. However, we submit that particularly in instances where a polished genome is not the primary goal of the sequencing project, PacBio SMRT sequencing provides a financially viable option for generating a biologically relevant genome estimate that can be utilized by other researchers for comparative studies.
authors.affiliation: Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
authors.forename: N
authors.initials: N
authors.lastname: Ricker
authors.affiliation: Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
authors.forename: S Y
authors.initials: SY
authors.lastname: Shen
authors.affiliation: Department of Natural Resource Sciences, McGill University, Macdonald Campus, 21111 Lakeshore Rd., Sainte Anne de Bellevue, Quebec H9X 3V9, Canada.
authors.forename: J
authors.initials: J
authors.lastname: Goordial
authors.affiliation: Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
authors.forename: S
authors.initials: S
authors.lastname: Jin
authors.affiliation: Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1095 Military Trail, Scarborough, Ontario M1C 1A4, Canada. Electronic address: fulthorpe@utsc.utoronto.ca.
authors.forename: R R
authors.initials: RR
authors.lastname: Fulthorpe
mesh_terms: D019117:Burkholderia / Q000235:genetics*; D002396:Catechols / Q000378:metabolism*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D009876:Operon; D012091:Repetitive Sequences, Nucleic Acid; D012093:Replicon; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D002396:Catechols
keywords: Burkholderia; Chlorocatechol degradation genes; Genome assembly; Mobile elements; Next generation sequencing; Plasmid