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Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.

Meyer JL, Dillard BA, Rodgers JM, Ritchie KB, Paul VJ, Teplitski M - Stand Genomic Sci (2015)

Bottom Line: Members of the gammaproteobacterial genus Halomonas are common in marine environments.Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals.The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.

View Article: PubMed Central - PubMed

Affiliation: Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA.

ABSTRACT
Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of select Halomonas type species and H. meridiana strain R1t3. The phylogenetic placement H. meridiana strain R1t3 in relation to select type species of marine and salt-tolerant Halomonas. Sequences from the 16S rRNA gene were aligned with MUSCLE and trimmed to 1154 bp, the length of the shortest sequence. Evolutionary history was inferred using the Maximum Likelihood method based on the Tamura-Nei model [26]. Branch lengths are measured in the number of substitutions per site. Branch labels indicate the percentage of trees in which the associated taxa were clustered based on 500 bootstraps using MEGA v 5.2.2 [27]. Genome sequences are not currently available for any of the type strains included in this figure
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Fig1: Phylogenetic tree of select Halomonas type species and H. meridiana strain R1t3. The phylogenetic placement H. meridiana strain R1t3 in relation to select type species of marine and salt-tolerant Halomonas. Sequences from the 16S rRNA gene were aligned with MUSCLE and trimmed to 1154 bp, the length of the shortest sequence. Evolutionary history was inferred using the Maximum Likelihood method based on the Tamura-Nei model [26]. Branch lengths are measured in the number of substitutions per site. Branch labels indicate the percentage of trees in which the associated taxa were clustered based on 500 bootstraps using MEGA v 5.2.2 [27]. Genome sequences are not currently available for any of the type strains included in this figure

Mentions: Within the polyphyletic family Halomonadaceae [10], Halomonas strain R1t3 is a member of the Group 2 assemblage, which may represent a separate genus, however defining characteristics have not been clearly determined for this potential revision [11]. The small subunit ribosomal RNA gene sequence of Halomonas strain R1t3 is nearly indistinguishable from the sequence in type strains of both H. meridiana and H. aquamarina (Fig. 1). Comparison of functional gene loci used in a previously published MLSA study [11] reveal that the loci secA, atpA, and rpoD are approximately 99 % identical between the two type strains and strain R1t3. In contrast, gene sequences for the gyrB locus are identical in the type strains, but only 87 % similar to the gyrB locus in strain R1t3. Strain R1t3 also exhibits high sequence identity to the small subunit ribosomal RNA gene to strain RA001 isolated from Acopora coral in India, and to uncultured Halomonas retrieved from Acropora corals in Mexico and Indonesia (Fig. 2).Fig. 1


Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.

Meyer JL, Dillard BA, Rodgers JM, Ritchie KB, Paul VJ, Teplitski M - Stand Genomic Sci (2015)

Phylogenetic tree of select Halomonas type species and H. meridiana strain R1t3. The phylogenetic placement H. meridiana strain R1t3 in relation to select type species of marine and salt-tolerant Halomonas. Sequences from the 16S rRNA gene were aligned with MUSCLE and trimmed to 1154 bp, the length of the shortest sequence. Evolutionary history was inferred using the Maximum Likelihood method based on the Tamura-Nei model [26]. Branch lengths are measured in the number of substitutions per site. Branch labels indicate the percentage of trees in which the associated taxa were clustered based on 500 bootstraps using MEGA v 5.2.2 [27]. Genome sequences are not currently available for any of the type strains included in this figure
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4597393&req=5

Fig1: Phylogenetic tree of select Halomonas type species and H. meridiana strain R1t3. The phylogenetic placement H. meridiana strain R1t3 in relation to select type species of marine and salt-tolerant Halomonas. Sequences from the 16S rRNA gene were aligned with MUSCLE and trimmed to 1154 bp, the length of the shortest sequence. Evolutionary history was inferred using the Maximum Likelihood method based on the Tamura-Nei model [26]. Branch lengths are measured in the number of substitutions per site. Branch labels indicate the percentage of trees in which the associated taxa were clustered based on 500 bootstraps using MEGA v 5.2.2 [27]. Genome sequences are not currently available for any of the type strains included in this figure
Mentions: Within the polyphyletic family Halomonadaceae [10], Halomonas strain R1t3 is a member of the Group 2 assemblage, which may represent a separate genus, however defining characteristics have not been clearly determined for this potential revision [11]. The small subunit ribosomal RNA gene sequence of Halomonas strain R1t3 is nearly indistinguishable from the sequence in type strains of both H. meridiana and H. aquamarina (Fig. 1). Comparison of functional gene loci used in a previously published MLSA study [11] reveal that the loci secA, atpA, and rpoD are approximately 99 % identical between the two type strains and strain R1t3. In contrast, gene sequences for the gyrB locus are identical in the type strains, but only 87 % similar to the gyrB locus in strain R1t3. Strain R1t3 also exhibits high sequence identity to the small subunit ribosomal RNA gene to strain RA001 isolated from Acopora coral in India, and to uncultured Halomonas retrieved from Acropora corals in Mexico and Indonesia (Fig. 2).Fig. 1

Bottom Line: Members of the gammaproteobacterial genus Halomonas are common in marine environments.Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals.The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.

View Article: PubMed Central - PubMed

Affiliation: Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA.

ABSTRACT
Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.

No MeSH data available.


Related in: MedlinePlus