Ricker_2016_Gene_586_239

Reference

Title : PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity - Ricker_2016_Gene_586_239
Author(s) : Ricker N , Shen SY , Goordial J , Jin S , Fulthorpe RR
Ref : Gene , 586 :239 , 2016
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.

PubMedSearch : Ricker_2016_Gene_586_239
PubMedID: 27063562
Gene_locus related to this paper: 9burk-a0a161ib31 , 9burk-a0a160ftv9 , 9burk-a0a160fin7 , 9burk-a0a160fk52

Related information

Citations formats

Ricker N, Shen SY, Goordial J, Jin S, Fulthorpe RR (2016)
PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity
Gene 586 :239

Ricker N, Shen SY, Goordial J, Jin S, Fulthorpe RR (2016)
Gene 586 :239