PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity

Ricker, Nicole; Shen, Shu Yi; Goordial, Jacqueline; Jin, Shaosheng; Fulthorpe, Roberta R.

doi:10.1016/j.gene.2016.04.018

Cited by 11 publications

(11 citation statements)

References 51 publications

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“…Long read sequencing technologies (ex- Moleculo, PacBIO) have been recently applied to generate soil (White et al, 2016 ) and skin (Tsai et al, 2016 ) metagenomes, and have proven advantageous to address the challenges of assembly and genomic binning in samples with low coverage regions or with diverse microbial communities. Similarly, other long read generating technology such as PacBIO have been found to be especially advantageous resolving genomic context when multiple replicons and large repetitive elements are present that make it inherently difficult to assemble by short read sequencing technologies (Ricker et al, 2016 ). Though not the focus of this paper, we were able to identify such a repetitive sequence (15 bp long) associated with an integron integrase in a 2,850 bp single molecule read from the MinION-generated ice wedge soil metagenome.…”

Section: Discussionmentioning

confidence: 99%

In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

et al. 2017

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Significant progress is being made in the development of the next generation of low cost life detection instrumentation with much smaller size, mass and energy requirements. Here, we describe in situ life detection and sequencing in the field in soils over laying ice wedges in polygonal permafrost terrain on Axel Heiberg Island, located in the Canadian high Arctic (79°26′N), an analog to the polygonal permafrost terrain observed on Mars. The life detection methods used here include (1) the cryo-iPlate for culturing microorganisms using diffusion of in situ nutrients into semi-solid media (2) a Microbial Activity Microassay (MAM) plate (BIOLOG Ecoplate) for detecting viable extant microorganisms through a colourimetric assay, and (3) the Oxford Nanopore MinION for nucleic acid detection and sequencing of environmental samples and the products of MAM plate and cryo-iPlate. We obtained 39 microbial isolates using the cryo-iPlate, which included several putatively novel strains based on the 16S rRNA gene, including a Pedobacter sp. (96% closest similarity in GenBank) which we partially genome sequenced using the MinION. The MAM plate successfully identified an active community capable of L-serine metabolism, which was used for metagenomic sequencing with the MinION to identify the active and enriched community. A metagenome on environmental ice wedge soil samples was completed, with base calling and uplink/downlink carried out via satellite internet. Validation of MinION sequencing using the Illumina MiSeq platform was consistent with the results obtained with the MinION. The instrumentation and technology utilized here is pre-existing, low cost, low mass, low volume, and offers the prospect of equipping micro-rovers and micro-penetrators with aggressive astrobiological capabilities. Since potentially habitable astrobiology targets have been identified (RSLs on Mars, near subsurface water ice on Mars, the plumes and oceans of Europa and Enceladus), future astrobiology missions will certainly target these areas and there is a need for direct life detection instrumentation.

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Section: Discussionmentioning

confidence: 99%

In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

et al. 2017

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“…The sequencing, assembly, and annotation pipeline previously described in our study on P. solitum RS1 (Yu et al., 2016) was used for the genome of P. expansum R19. Briefly, the assembly was conducted using HGAP3 under default settings, which applies long read correction algorithms and the Celera assembler to confidently produce high quality contigs (unitigs) using reads from PacBio Single Molecule Real Time (SMRT) sequencing technology (Ricker et al., 2016). The annotation software MAKER (Holt & Yandell, 2011) was implemented for four iterative runs starting with gene predictions from CEGMA (Parra, Bradnam & Korf, 2007).…”

Section: Methodsmentioning

confidence: 99%

Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay

Jurick

Lichtner

et al. 2019

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Blue mold is a postharvest rot of pomaceous fruits caused by Penicillium expansum and a number of other Penicillium species. The genome of the highly aggressive P. expansum strain R19 was re-sequenced and analyzed together with the genome of the less aggressive P. solitum strain RS1. Whole genome scale similarities and differences were examined. A phylogenetic analysis of P. expansum, P. solitum, and several closely related Penicillium species revealed that the two pathogens isolated from decayed apple with blue mold symptoms are not each other’s closest relatives. Among a total of 10,560 and 10,672 protein coding sequences respectively, a comparative genomics analysis revealed 41 genes in P. expansum R19 and 43 genes in P. solitum RS1 that are unique to these two species. These genes may be associated with pome fruit–fungal interactions, subsequent decay processes, and mycotoxin accumulation. An intact patulin gene cluster consisting of 15 biosynthetic genes was identified in the patulin producing P. expansum strain R19, while only a remnant, seven-gene cluster was identified in the patulin-deficient P. solitum strain. However, P. solitum contained a large number of additional secondary metabolite gene clusters, indicating that this species has the potential capacity to produce an array of known as well as not-yet-identified products of possible toxicological or biotechnological interest.

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“…Single Molecule Real Time (SMRT) DNA sequencing (Pacific Biosciences) has emerged as a leading technology for characterizing complex structural variations, supporting and refining the assembly of complex genomes in hybrid fashion or alone for reconstructing highly continuous assemblies of both small and highly repetitive genomes (Chin et al, 2013; Doi et al, 2014; Huddleston et al, 2014, 2016; Gordon et al, 2016; Ricker et al, 2016; Seo et al, 2016; Vij et al, 2016). The advantage of SMRT technology arises from the delivery of long reads, currently averaging over 30 kbp and potentially approaching 100 kbp.…”

Section: Recent Developments In Grape Genome Sequencingmentioning

confidence: 99%

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes

et al. 2017

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PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity

Cited by 11 publications

References 51 publications

In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes

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