- gigas larvae. - Knowledge of the specific nature of these factors is essential to developing a better understanding of the environmental and biological conditions that lead to larvae mortality events in hatcheries. - gigas larvae.. - broadly referred to as “vibriosis”, with the identities of the etiological agents and their pathogenic mechanisms varying between hosts. - Genomic sequencing of marine pathogens has aided our understanding of the genetic mechanisms of virulence in some of these systems. - Full list of author information is available at the end of the article. - gigas larvae [27]. - Members of the high-pathogenicity group consistently caused larvae mortalities between 51 and 100% and primarily included isolates identified as V. - To better understand the genomic potential of hatchery-associated vibrios and identify traits that are associated with virulence, we conducted whole-genome shotgun sequencing, assembly, and annotation of the 42 isolates (Table 1). - 2), and clusters most of the isolates into two main clades: the Coralliilyticus clade and the Splendidus clade. - These data were con- gruent with a phylogenetic tree built from concatenated sequences of the computationally-determined core gen- ome of 154 Vibrionaceae genomes (Additional file 3:. - distance of 0.209.. - The core, flex, and pan-genomes of isolate genomes were classified to determine the functional composition of the conserved and unique genes. - S3), and the curve of the pan-genome plot and the Heaps law model (alpha = 0.47) indicated an open-pan genome amongst these isolates.. - The observed distribution of functional categories of the genes significantly correlated with the results of larval pathogenicity assays was significantly different than that of the genes in the core genome (chi-square = 3979.2, df = 19, p <. - Since most of the patho- genic isolates were putatively assigned as V. - The putative reb genes were located within a larger putative genomic is- land of the RE22 complete genome. - Table 1 Bacterial strains and genomes used in this study. - alginolyticus 062916C 2016 Oregon This study* VTYI00000000. - alginolyticus 081416A 2016 Oregon This study* VTYF00000000. - alginolyticus L22Y01 2015 Washington This study* VTYJ00000000. - anguillarum Washington This study* VTYO00000000. - chagasii Hawaii This study* VTXW00000000. - coralliilyticus 071316B 2016 Oregon This study* VTYG00000000. - coralliilyticus 081216C 2016 Oregon This study* VTYE00000000. - coralliilyticus Unknown Unknown This study* VTXP00000000. - coralliilyticus AIC-5 2015 New Jersey This study* VTXB00000000. - coralliilyticus C154 2017 Washington This study* VTYL00000000. - crassostreae Washington This study* VTXY00000000. - cyclitrophicus T6Y01 2015 Washington This study* VTYK00000000. - cyclitrophicus 070116B 2016 Oregon This study* VTYB00000000. - hepatarius 070516A 2016 Oregon This study* VTYD00000000. - jasicida T3G01 2015 Washington This study* VTXQ00000000. - kanaloae 073016A 2016 Oregon This study* VTXS00000000. - mediterranei Hawaii This study* VTXV00000000. - mediterranei 71105 Unknown Florida This study* VTXU00000000. - owensii Hawaii This study* VTXX00000000. - rotiferianus Hawaii This study* VTYN00000000. - rotiferianus Hawaii This study* VTXT00000000. - 070316B 2016 Oregon This study* VTYC00000000. - pectenicida 99 – 46-Y 2000 Washington This study* VTXC00000000. - 99 – 70-13A1 2000 Oregon This study* VTXD00000000. - Washington This study* VTXE00000000. - 99 K-1 2000 Hawaii This study* VTXF00000000. - AIC-3 2016 New Jersey This study* VTXG00000000. - aestuarianus O-00-16-10 Unknown Washington This study* VTXH00000000. - splendidus T3Y01 2015 Washington This study* VTXJ00000000. - Within the large chromosome of the RE22 genome, a number of syntenic loci whose presences were sig- nificantly negatively correlated with larvae survival had annotations for a functional Type 3 Secretion System (T3SS. - In addition to encoding a T3SS and effec- tors, this region includes genes for multiple Table 1 Bacterial strains and genomes used in this study (Continued). - splendidus California This study* VTXK00000000. - splendidus 99 – 70-13A3 2000 Oregon This study* VTXL00000000. - splendidus 99 – 70-6B3 2000 Oregon This study* VTXM00000000. - splendidus X Oregon This study* VTXN00000000. - tubiashii Hawaii This study* VTXO00000000. - A comparison of the CPI-1 region of six V. - Phylogenetic analysis of the sctV gene, which encodes a conserved protein of the T3SS, indicated that this gene is more similar to those of species of Yersinia, Salmonella, Escherichia, Edwardsiella and Shewanella,. - 3 Manhattan Plot with P-value results for Vibrio genes correlating with larvae mortalities and ACT plots of the CPI-1 region of six V.. - Compara- tive analysis of the genomes of these 51 isolates identi- fied genes specifically associated with a pathogenic lifestyle from the large pan-genome. - Table 2 Features of the putative Reb-coding region of Vibrio coralliilyticus strain RE22 V. - gigas larvae, so although we attempted to control for phylo- genetic signal with the phylolm package, we cannot definitively assert that the genes detected with this model are directly related to pathogenesis rather than just being a trait of the species serving some other ecological function. - A number of gene clusters negatively correlated with oyster survival were homologous to genes of the CPI-1 pathogenicity island of V. - This allows for a com- parison of the gene content of the CPI-1 from pathogens with that of the CPI-1 of V. - which are known to cause epithelial damage and contribute to intestinal growth of the bacterium [37]. - coralliilyticus is known to cause a decline in feeding rate, an activation of the immune response (e.g., hematopoiesis, activation of non-self recognition mechanisms, and production of antimicrobial peptides), and modulation of cell membrane composition [26].. - For instance, multiple genes of a ~ 30 Kb-long locus conserved within the genomes of the tested V. - R-bodies of the intracellular symbiont, Caedibacter, switch between two stable conformations in response to a stimulus such as an extracellular pH change that occurs during phago- cytosis. - coralliilyticus infections may be facilitated by invading and/or modulating the cells of the oyster im- mune system.. - An additional caveat of our work is that gene clusters detected as in-paralogs, such as one of the T6SS clusters present in many genomes of pathogens, were not analyzed with the phylogenetic logistic regression precluding direct comparisons with previous results.. - coralliilyticus infection of the coral Pocillo- pora damicornis and of V. - The genetic features described here will be fruitful targets for future mechanistic studies of the oyster larvae pathogenesis.. - Forty-two newly sequenced hatchery- associated Vibrio genomes are presented in this study.. - Briefly, neutral red solution was added to each well at a final concentration of 0.0002% (v/v). - High quality reads were then randomly subsampled to obtain approximately 50-fold coverage of the genome and assembled using IDBA-UD version with it- erative k-mer assembly between a 45 and 105 with 4-mer increments. - A 95% ANI cut-off ratio to reference genomes was used to putatively assign species labels to each of the newly sequenced genomes [74–76].. - of the 51 genomes analyzed. - The “flex genome” was defined as those genes present in 5–95% of the genomes.. - RAxML was used to build a partitioned maximum likelihood phylo- genetic tree from this alignment, using a GAMMA distribution of rate heterogeneity and individually esti- mated models of evolution for each gene partition of the concatenated alignment [85].. - OrthoMCL was used to cluster protein sequences with 50% minimum coverage, 50% minimum identity and a default e-value of 0.00001. - To identify the set of genes in Vibrio genomes signifi- cantly associated with larvae mortalities, correlations between presence or absence of genes and the results of larval pathogenicity assays were calculated with a phylo- genetic logistic regression model of the R package “phy- lolm” (86). - Gene occurrences were considered significantly correlated with larvae data using a p-value cutoff of 0.005, and the effect of the relationship was determined by the strength and sign of the correlation estimate.. - Heatmap and dendrogram of Average Nucleotide Identity (ANI) calculations between pairs of different Vibrio strains, including strains used in this study and reference strains. - Phylogenetic Tree of strains used in this study and reference strains. - Core and Pan-genome of 51 isolates in this study. - Gene organization of the CPI-1 region within the complete genome of V. - Yellow slashed lines indicate contig breaks on the CPI-1 of the V. - HD was a recipient of the OSU Tartar Fellowship and John Fryer Scholarship. - The funding bodies were not involved in design of the study and collection, analysis, and interpretation of results or in writing the manuscript.. - The draft genomes of the 42 Vibrio isolates have been deposited in the GenBank database under project accession no. - A review of the main bacterial fish diseases in mariculture systems. - pathogen of the coral Pocillopora damicornis. - nov., a temperature-dependent pathogen of the coral Pocillopora damicornis. - Mutation of the toxR or mshA genes from Vibrio coralliilyticus strain OCN014 reduces infection of the coral Acropora cytherea: virulence genes in Vibrio coralliilyticus. - The antimicrobial defense of the pacific oyster, crassostrea gigas.. - Comparative Transcriptome analysis reveals molecular basis underlying fast growth of the selectively bred Pacific oyster, Crassostrea gigas. - Transcriptome analysis of the pearl oyster ( Pinctada fucata ) hemocytes in response to Vibrio alginolyticus infection. - Conservation of the chitin utilization pathway in the Vibrionaceae. - Identification of chitin in the prismatic layer of the Shell and a chitin synthase gene from the Japanese pearl oyster, Pinctada fucata. - Biomineralization-related specialization of hemocytes and mantle tissues of the Pacific oyster Crassostrea gigas. - Genomic and proteomic analyses of the coral pathogen Vibrio coralliilyticus reveal a diverse virulence repertoire. - Physiological responses of the scleractinian coral Pocillopora damicornis to bacterial stress from Vibrio coralliilyticus
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