Journal: bioRxiv

Article Title: Closing the genome of Teredinibacter turnerae T7902 by long-read nanopore sequencing

doi: 10.1101/2024.07.30.605897

Figure Lengend Snippet: Synteny plot comparing the previously published genome of T. turnerae T7902 (GCA_000379165.1) and the new genome sequence and assembly presented here (GCA_037935975.1). A MUMmer3 plot was generated with NUCmer v3.1 using default settings to assess synteny and completion. Minimum exact matches of 20bp are represented as a dot with lines representing exact match lengths >20bp. Forward matches are displayed in red, while reverse matches are shown in blue.

Article Snippet: We present the complete closed circular genome sequence derived from Oxford Nanopore sequencing of the shipworm endosymbiont Teredinibacter turnerae T7902 (DSM 15152, ATCC 39867), originally isolated from the shipworm Lyrodus pedicellatus ( ).

Techniques: Sequencing, Generated

Journal: bioRxiv

Article Title: The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, reveals the potential for hydrocarbon degradation and CRISPR-Cas defense

doi: 10.1101/2024.10.01.616199

Figure Lengend Snippet: (A) Phylogenomic tree of bacteria in the genus Gallaecimonas based on data in NCBI Reference Sequence Database (RefSeq, v.216). The tree was built based on the overall genome sequences and rooted with two genome sequences from Escherichia coli (GTDBtk accession numbers: RS GCF 011881725.1 and RS GCF 003697165.2) as an outgroup. (B) Phylogenetic relationship of the 16S rRNA gene sequences from strain 10A and other Gallaecimonas spp. found in the SILVA rRNA gene database v.138.1. The maximum-likelihood tree was built using 100 replicates and rooted with sequences from two strains of Escherichia coli (NCBI accession number: CP033092 and MT215717 ) as an outgroup. The value in the heatmaps associated with the phylogenic tree represents the average nucleotide identity (ANI) of 16S rRNA gene sequences between two strains on each of the x and y axes.

Article Snippet: Phylogenomic analysis based on whole genomes of Gallaecimonas spp. are consistent with strain 10A being closely related to G. pentaromativorans strain CEE_131 (Leibniz Institute DSMZ culture collection ID: DSM21945; ).

Techniques: Bacteria, Sequencing

Journal: bioRxiv

Article Title: The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, reveals the potential for hydrocarbon degradation and CRISPR-Cas defense

doi: 10.1101/2024.10.01.616199

Figure Lengend Snippet: (A) Comparative map depicting genomic arrangements of four other isolates of Gallaecimonas spp. to strain 10A. (B) Venn diagram illustrating the distribution of shared and unique genes among the five strains of Gallaecimonas spp. (C) Key functional pathways found in G. pentaromativorans strain 10A, including PAHs and xenobiotic degradation, methanol oxidation, nitrate assimilation, sulfur metabolism, higB-1/higA-1 toxin-antitoxin system, and biosurfactant-producing pathways.

Article Snippet: Phylogenomic analysis based on whole genomes of Gallaecimonas spp. are consistent with strain 10A being closely related to G. pentaromativorans strain CEE_131 (Leibniz Institute DSMZ culture collection ID: DSM21945; ).

Techniques: Functional Assay

Journal: bioRxiv

Article Title: The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, reveals the potential for hydrocarbon degradation and CRISPR-Cas defense

doi: 10.1101/2024.10.01.616199

Figure Lengend Snippet: Detection of CRISPR-Cas systems in Gallaecimonas spp. Operon organization of different CRISPR-Cas systems detected in genomes of Gallaecimonas spp., annotated with the clustered regularly interspaced short palindromic repeats (CRISPR), spacers, and CRISPR- associated (Cas) proteins. Annotations are based on sequence similarities to known Cas proteins using HMM protein profiles and identified using CRISPRFinder.

Article Snippet: Phylogenomic analysis based on whole genomes of Gallaecimonas spp. are consistent with strain 10A being closely related to G. pentaromativorans strain CEE_131 (Leibniz Institute DSMZ culture collection ID: DSM21945; ).

Techniques: CRISPR, Sequencing

Journal: bioRxiv

Article Title: The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, reveals the potential for hydrocarbon degradation and CRISPR-Cas defense

doi: 10.1101/2024.10.01.616199

Figure Lengend Snippet: (A) The global distribution of 16S rRNA gene sequences assigned to Gallaecimonas spp. was assessed using 536 sequences sourced from the GBIF Database. Orange and green indicate sequences assigned to G. pentaromativorans and G. xiamenensis , respectively, while “Other Gallaecimonas ” comprises G. kandeliae , G. mangrove , and unclassified Gallaecimonas spp. The circle size represents the relative abundance of sequences assigned to Gallaecimonas spp. within the prokaryotic community. (B) The proportion of 16S rRNA gene sequences assigned to Gallaecimonas spp. across environments. Seawater, estuary, and freshwater correspond to water samples from the respective environments. Polar represents the cryosphere, and sediment includes samples from marine (e.g., pelagic sediment cores, benthic continental shelf), rivers, wetlands, saltmarshes, and tidal mudflats.

Article Snippet: Phylogenomic analysis based on whole genomes of Gallaecimonas spp. are consistent with strain 10A being closely related to G. pentaromativorans strain CEE_131 (Leibniz Institute DSMZ culture collection ID: DSM21945; ).

Techniques: