GENOME ANNOUNCEMENT
Complete Genome Sequence of the Copiotrophic Marine Bacterium Alteromonas macleodii Strain ATCC 27126T Aitor Gonzaga, Mario López-Pérez, Ana-Belen Martin-Cuadrado, Rohit Ghai, and Francisco Rodriguez-Valera Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, Alicante, Spain
The genome of Alteromonas macleodii strain ATCC 27126T has been resequenced and closed into a single contig. We describe here the genome of this important and globally distributed marine bacterium.
lteromonas macleodii ATCC 27126T is one of the first isolates described as a marine bacterium. It was obtained by Baumann and coworkers from waters off Oahu, HI, and published in 1972 (2). It is a strictly aerobic gammaproteobacterium (family Alteromonadaceae), motile by one unsheathed polar flagellum and capable of growing on glucose as the only carbon and energy source. Like many marine microbes, it requires a relatively high sodium concentration for growth. This microbe has been shown to have a global distribution in marine temperate or tropical environments (3) and becomes very abundant when a high concentration of nutrients becomes available, e.g., when water is enclosed in a mesocosm (10) or in microniches near marine snow and other marine particulate organic matter (1–7). Recent evidence indicates that its growth is highly enhanced by enriching surface seawater with deep water samples (11) or by adding natural marine dissolved organic matter (9). A relative of this original isolate was obtained from the deep Mediterranean, and its genome was fully sequenced and assembled (5). A draft genome of ATCC 27126T produced by low-coverage 454 pyrosequencing was used for comparison but only allowed the assembly of this genome, the one of the species type strain (2), in 716 contigs. The genome of the ATCC 27126T strain has now been fully sequenced using a combination of 454 GS-FLX Titanium platform (Roche Applied Science) and Illumina GAIIx technologies. 454 generated 123,975,124 reads, which represented a 27-fold coverage of the genome, and paired-end 454 libraries with an average insert size of 2,922 produced 500,025 reads. The 454 data were assembled using the Newbler assembler (version 2.3) into 36 contigs. In addition, 937,214,537 reads (average read length, 38 bp) produced in the Illumina library and the 716 contigs previously obtained (5) were assembled using Geneious Pro 5.0.1 (with default parameters) to fill the gaps and improve the quality of the sequence. Oligonucleotides were designed from the ends of assembled contigs, and PCR amplicons were sequenced in order to concatenate them into one single circular chromosome 4,655,697 bp long with 47% GC content. No plasmids were found. Integrative Services for Genomic Analysis (ISGA) (4) was used, producing 4,181 predicted protein-coding sequences, 54 tRNA genes, and 5 complete rRNA loci. Genes encoding tRNAs and rRNA operons were determined by tRNAscan-SE (6) and RNAmmer 1.2 (8), respectively. Nucleotide sequence accession number. The complete genome sequence of Alteromonas macleodii strain ATCC 27126T has been deposited in GenBank under accession no. CP003841.
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ACKNOWLEDGMENTS This work was supported by projects MAGYK (BIO2008-02444), MICROGEN (Programa CONSOLIDER-INGENIO 2010 CDS2009-00006), CGL2009-12651-C02-01 from the Spanish Ministerio de Ciencia e Innovación, DIMEGEN (PROMETEO/2010/089) and ACOMP/2009/155 from the Generalitat Valenciana, and MaCuMBA Project 311975 of the European Commission FP7. FEDER funds supported this project. R.G. was supported by a Juan de la Cierva scholarship from the Spanish Ministerio de Ciencia e Innovación.
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Received 26 August 2012 Accepted 4 October 2012 Address correspondence to Francisco Rodriguez-Valera,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01565-12
December 2012 Volume 194 Number 24
