Proksee: in-depth characterization and visualization of bacterial genomes

Grant, Jason R.; Enns, Eric; Marinier, Eric; Mandal, Arnab; Herman, Emily K.; Chen, Chih-Yu; Graham, Morag; Domselaar, Gary Van; Stothard, Paul

doi:10.1093/nar/gkad326

Cited by 497 publications

(191 citation statements)

References 25 publications

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“…Horizontal, black lines indicate contig joins informed by the Hi-C sequencing data. B) Circos plot of the southern stuttering frog mitochondrial genome generated using Proksee (Grant et al 2023). Outer ring contains genes on the forward strand, while the inner ring contains genes on the reverse strand.…”

Section: Resultsmentioning

confidence: 99%

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Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

Tang,

Peel,

Belov

et al. 2023

Preprint

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The number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and β-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two beta-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.

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Section: Resultsmentioning

confidence: 99%

“…From the assembly, we identified a scaffold representing the mitochondrial genome, which contained 36 genes: 21 tRNAs, 2 rRNAs and 13 protein-coding genes (Figure 1B). (Grant et al 2023). Outer ring contains genes on the forward strand, while the inner ring contains genes on the reverse strand.…”

Section: Multi-omics Resources For the Southern Stuttering Frogmentioning

confidence: 99%

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

Tang,

Peel,

Belov

et al. 2023

Preprint

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“…Presence/absence matrices were created for each of these pathways before being plotted using pHeatmap. Proksee (47) was then used to visualise the circular chromosome of Erwimp and ORFs found in PathwayTools were then annotated in Inkscape v1.1 (48). Clinker (49) plotted the similarity of carotenoid biosynthetic genes discovered using AntiSMASH.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics of a novelErwiniaspecies associated with the Highland midge (Culicoides impunctatus)

Pilgrim

2023

Preprint

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2.AbstractErwinia(Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in the group have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describeCandidatusErwinia impunctatus (Erwimp) associated with the Highland midgeCulicoides impunctatus(Diptera: Ceratopogonidae), an abundant biting pest in the Scottish Highlands. The genome of this newErwiniaspecies was assembled using hybrid long and short read techniques, and a comparative analysis was undertaken with other members of the genus to understand its potential ecological niche and impact. Genome composition analysis revealed that Erwimp is similar to other endophytic and ectophytic species in the genus and is unlikely to be restricted to its insect host. Evidence for an additional plant host includes the presence of a carotenoid synthesis operon implicated as a virulence factor in plant-associated members in the sister genusPantoea. Unique features of Erwimp include several copies of intimin-like proteins which, along with signs of genome pseudogenization and a loss of certain metabolic pathways, suggests an element of host restriction seen elsewhere in the genus. Furthermore, a screening of individuals over two field seasons revealed the absence of the bacteria inC. impunctatusin the second year indicating this microbe-insect interaction is likely to be transient. These data suggest thatCulicoides impunctatusmay have an important role to play beyond a biting nuisance, as an insect vector transmitting Erwimp alongside any conferred impacts to surrounding biota.

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“…The complete genome was manually selected using minimap2 version 2.24-r1122 (Li, 2018) and blobtools version 1.1.1 (Laetsch & Blaxter, 2017). The general information of the symbiont genome was visualized using Proksee (Grant et al, 2023). Single-nucleotide polymorphisms (SNPs) in the symbiont were detected using a pipeline published by Lan et al (2022)…”

Section: Genome Sequencing Assembly Binning and Snp Callingmentioning

confidence: 99%

Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment

Wang

Lin

et al. 2023

Molecular Ecology Resources

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Previous studies have deciphered the genomic basis of host‐symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae—a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep‐sea and shallow‐water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free‐living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well‐adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen‐adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.

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Proksee: in-depth characterization and visualization of bacterial genomes

Cited by 497 publications

References 25 publications

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

Comparative genomics of a novelErwiniaspecies associated with the Highland midge (Culicoides impunctatus)

Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment

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