Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h

Merga, J. Yvette; Winstanley, Craig; Williams, Nicola; Yee, Emma; Miller, William G.

doi:10.1128/genomea.00655-13

Cited by 18 publications

(21 citation statements)

References 11 publications

(11 reference statements)

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“…First, for each genome, shotgun and paired-end 454 reads were assembled using the Roche Newbler assembler (v 2.6) into a single chromosomal scaffold. Each scaffold was closed into one contiguous sequence, using the 454 repeat contigs and the Perl script contig_extender3 ([ Merga et al 2013 ]; see also supplementary File S1 , Supplementary Material online); contig gaps/junctions within each scaffold were also validated using PCR amplification and Sanger sequencing. Second, Illumina HiSeq or MiSeq reads were assembled de novo within Newbler; these Illumina contigs were assembled into the 454 assembly within Seqman (v. 8.0.2) to validate all 454 base calls.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Miller

Yee

Lopes

et al. 2017

Genome Biology and Evolution

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The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g., cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group was conducted (including average nucleotide identity analysis) that supports the initial identification of these three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems. Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but nonidentical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins, and the selenocysteinyl tRNA.

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Section: Methodsmentioning

confidence: 99%

Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism

Miller

Yee

Lopes

et al. 2017

Genome Biology and Evolution

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“…Shotgun and paired-end 454 reads were assembled using the Roche Newbler assembler (v2.6) into one or two chromosomal scaffolds, providing draft genome sequences with a coverage of 35–136× ( table 1 ). Intrascaffold gaps were filled using the 454 repeat contigs and the Perl script contig_extender3 ( Merga et al 2013 ). Contig gaps were closed/validated using PCR amplification and Sanger sequencing, generating draft pseudomolecules for each genome.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of the Campylobacter lari Group

Miller

Yee

Chapman

et al. 2014

Genome Biology and Evolution

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The Campylobacter lari group is a phylogenetic clade within the epsilon subdivision of the Proteobacteria and is part of the thermotolerant Campylobacter spp., a division within the genus that includes the human pathogen Campylobacter jejuni. The C. lari group is currently composed of five species (C. lari, Campylobacter insulaenigrae, Campylobacter volucris, Campylobacter subantarcticus, and Campylobacter peloridis), as well as a group of strains termed the urease-positive thermophilic Campylobacter (UPTC) and other C. lari-like strains. Here we present the complete genome sequences of 11 C. lari group strains, including the five C. lari group species, four UPTC strains, and a lari-like strain isolated in this study. The genome of C. lari subsp. lari strain RM2100 was described previously. Analysis of the C. lari group genomes indicates that this group is highly related at the genome level. Furthermore, these genomes are strongly syntenic with minor rearrangements occurring only in 4 of the 12 genomes studied. The C. lari group can be bifurcated, based on the flagella and flagellar modification genes. Genomic analysis of the UPTC strains indicated that these organisms are variable but highly similar, closely related to but distinct from C. lari. Additionally, the C. lari group contains multiple genes encoding hemagglutination domain proteins, which are either contingency genes or linked to conserved contingency genes. Many of the features identified in strain RM2100, such as major deficiencies in amino acid biosynthesis and energy metabolism, are conserved across all 12 genomes, suggesting that these common features may play a role in the association of the C. lari group with coastal environments and watersheds.

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“…The de novo large contigs and the contigs derived from the reference assembly were used to create a draft scaffold. The scaffold gaps were filled using the small-repeat de novo contigs and the Perl script Contig_extender3 ( 8 ). The final genomic sequences had coverages of 325× (RM3196) and 322× (RM3197).…”

Section: Genome Announcementmentioning

confidence: 99%