Evidence map›Paper›PMID 28145490›Full record

ArticleScientific reports2017

Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade.

Huei-Mien Ke, Anuphap Prachumwat, Chun-Ping Yu, Yi-Ting Yang, Sutitcha Promsri, Kuan-Fu Liu, Chu-Fang Lo, Mei-Yeh Jade Lu, Mei-Chin Lai, Isheng J Tsai and 1 more

Abstract readComparative Study
In one paragraph

Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

25 citing papers in PubMed.

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  16. Marine life science & technology · 2020
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  17. Phylogenetic Relationship Among BrackishwaterEvolutionary bioinformatics online · 2020
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Huei-Mien KePh.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.
Anuphap PrachumwatCentex Shrimp, Faculty of Science, Mahidol University, Bangkok, Thailand.
Chun-Ping YuBiodiversity Research Center, Academia Sinica, Taipei, Taiwan.
Yi-Ting YangInstitute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
Sutitcha PromsriCentex Shrimp, Faculty of Science, Mahidol University, Bangkok, Thailand.
Kuan-Fu LiuTungkang Biotechnology Research Center, Fisheries Research Institute, Council of Agriculture, Pingtung, Taiwan.
Chu-Fang LoInstitute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
Mei-Yeh Jade LuBiodiversity Research Center, Academia Sinica, Taipei, Taiwan.
Mei-Chin LaiPh.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.
Isheng J TsaiPh.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.
Wen-Hsiung LiPh.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.

Indexed as

Genome, BacterialGenomicsPhylogenyBase SequenceDNA Transposable ElementsGene DosageGenes, BacterialSelection, GeneticSequence Analysis, DNASpecies SpecificitySyntenyVibrioDNA Transposable Elements

Identifiers

PMID28145490
PMCPMC5286417

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.