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Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria.

Huggett MJ, Hayakawa DH, Rappé MS - Stand Genomic Sci (2012)

View Article: PubMed Central - PubMed

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Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii... This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43... Strain HIMB624 was isolated from surface seawater of Kaneohe Bay, a subtropical bay on the northeastern shore of Oahu, Hawaii, via dilution to extinction culturing methods... This strain is of interest because it belongs to a globally ubiquitous clade of aquatic bacterioplankton known as OM43, within the obligately methylotrophic family Methylophilaceae of the class Betaproteobacteria... The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases... The tRNAScanSE tool was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer... The genomes of HIMB624 and HTCC2181 were compared to two closely related species within the family Methylophilaceae whose whole genomes are publicly available: Methylotenera mobilis (NC_012968) and Methylovorus glucosotrophus SIP3-4 (NC_012969, NC_012970, NC_012972)... For this comparison only, the four strains were automatically annotated using the RAST annotation server and protein sequences were compared using the sequence based analysis tool in order to identify all shared and unique gene combinations (Figure 4)... Strain HIMB624 contains one gene for a Type 4 fimbrial assembly/ATPase PilB that shares 43.44% protein identity with a gene located on one of the plasmids of Methylovorus glucosotrophus SIP3-4, and strain HTCC2181 contains a single DNA methylase gene that shares 31.1% protein identity with the same plasmid... Other than these, all genes located on the plasmids are exclusive to Methylovorus glucosotrophus SIP3-4, and the large majority of the genes on the plasmids are hypothetical proteins... The genomes of Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4 share over 100 genes associated with motility (twitching, flagella related, pili), along with 13 genes for chemotaxis and 13 genes for secretion that are absent from the genomes of HIMB624 and HTCC2181, while the two smaller genomes have a higher percentage of their genomes (9.13% and 9.19%) dedicated to amino acid transport and metabolism than Methylovorus glucosotrophus SIP3-4 (6.76%) and Methylotenera mobilis (5.81%); and a higher percentage of translation, ribosomal structure and biogenesis genes (11.08% and 11.47%) than Methylovorus glucosotrophus SIP3-4 (6.12%) and Methylotenera mobilis (7.16%)... Due to the small size of the two OM43 lineage genomes, the higher percentages result in a similar total number of genes between all genomes in these categories, at approximately 120 genes for amino acid transport and metabolism and approximately 140 genes for translation, ribosomal structure and biogenesis... The general distribution of genes in all other predicted COG categories are comparable between the four strains, resulting in smaller numbers of total genes in each COG category for the two members of the OM43 lineage due to their comparatively smaller genome sizes.

No MeSH data available.


Graphic circular map of the HIMB624 genome. From outside to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.
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f3: Graphic circular map of the HIMB624 genome. From outside to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Mentions: The genome is 1,333,209 bp long and comprises four contigs in a single scaffold, with an overall GC content of 35.37% (Table 3 and Figure 3). Of the 1,420 genes predicted, 1,381 were protein-coding genes and 39 were RNAs. The majority (83.59%) of the protein coding genes was assigned with a putative function, while the remaining genes were annotated as hypothetical proteins. The distribution of genes into COGS functional categories is presented in Table 4.


Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria.

Huggett MJ, Hayakawa DH, Rappé MS - Stand Genomic Sci (2012)

Graphic circular map of the HIMB624 genome. From outside to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3368401&req=5

f3: Graphic circular map of the HIMB624 genome. From outside to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.
Mentions: The genome is 1,333,209 bp long and comprises four contigs in a single scaffold, with an overall GC content of 35.37% (Table 3 and Figure 3). Of the 1,420 genes predicted, 1,381 were protein-coding genes and 39 were RNAs. The majority (83.59%) of the protein coding genes was assigned with a putative function, while the remaining genes were annotated as hypothetical proteins. The distribution of genes into COGS functional categories is presented in Table 4.

View Article: PubMed Central - PubMed

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii... This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43... Strain HIMB624 was isolated from surface seawater of Kaneohe Bay, a subtropical bay on the northeastern shore of Oahu, Hawaii, via dilution to extinction culturing methods... This strain is of interest because it belongs to a globally ubiquitous clade of aquatic bacterioplankton known as OM43, within the obligately methylotrophic family Methylophilaceae of the class Betaproteobacteria... The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases... The tRNAScanSE tool was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer... The genomes of HIMB624 and HTCC2181 were compared to two closely related species within the family Methylophilaceae whose whole genomes are publicly available: Methylotenera mobilis (NC_012968) and Methylovorus glucosotrophus SIP3-4 (NC_012969, NC_012970, NC_012972)... For this comparison only, the four strains were automatically annotated using the RAST annotation server and protein sequences were compared using the sequence based analysis tool in order to identify all shared and unique gene combinations (Figure 4)... Strain HIMB624 contains one gene for a Type 4 fimbrial assembly/ATPase PilB that shares 43.44% protein identity with a gene located on one of the plasmids of Methylovorus glucosotrophus SIP3-4, and strain HTCC2181 contains a single DNA methylase gene that shares 31.1% protein identity with the same plasmid... Other than these, all genes located on the plasmids are exclusive to Methylovorus glucosotrophus SIP3-4, and the large majority of the genes on the plasmids are hypothetical proteins... The genomes of Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4 share over 100 genes associated with motility (twitching, flagella related, pili), along with 13 genes for chemotaxis and 13 genes for secretion that are absent from the genomes of HIMB624 and HTCC2181, while the two smaller genomes have a higher percentage of their genomes (9.13% and 9.19%) dedicated to amino acid transport and metabolism than Methylovorus glucosotrophus SIP3-4 (6.76%) and Methylotenera mobilis (5.81%); and a higher percentage of translation, ribosomal structure and biogenesis genes (11.08% and 11.47%) than Methylovorus glucosotrophus SIP3-4 (6.12%) and Methylotenera mobilis (7.16%)... Due to the small size of the two OM43 lineage genomes, the higher percentages result in a similar total number of genes between all genomes in these categories, at approximately 120 genes for amino acid transport and metabolism and approximately 140 genes for translation, ribosomal structure and biogenesis... The general distribution of genes in all other predicted COG categories are comparable between the four strains, resulting in smaller numbers of total genes in each COG category for the two members of the OM43 lineage due to their comparatively smaller genome sizes.

No MeSH data available.