Genome Sequence of the Marine Bacterium Marinilabilia salmonicolor JCM 21150^T

Abstract

We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150^T, which was isolated from marine mud in the year 1961. The draft genome of strain Marinilabilia salmonicolor JCM 21150^T contains 4,982,627 bp with a G+C content of 41.92% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.

GENOME ANNOUNCEMENT

Marinilabilia salmonicolor JCM 21150^T was isolated from marine mud in the year 1961, and it is the only type strain of the genus Marinilabilia isolated to date. Cells of the strain JCM 21150^T are long slender rods of 0.3 to 0.5 μm in width and 2 to 50 μm in length. The strain is capable of gelatin liquefaction. All the strains of the genus Marinilabilia were reported to decompose various biomacromolecules (4).

The genome of Marinilabilia salmonicolor JCM 21150^T was sequenced using Illumina-HiSeq 1000 technology. A total of 35,195,778 paired-end reads (insert size, 350 bp) of 101 nucleotides in length were obtained. We used the NGS QC toolkit v2.2.1 (5) to filter the data for high-quality (HQ) (cutoff read length for HQ, 70%; cutoff quality score, 20), vector/adaptor-free reads for genome assembly. A total of 30,926,566 high-quality, vector-filtered reads (∼618× coverage) were used for assembly with Velvet 1.2.03 (at a hash length of 65) (6). The final assembly contains 72 contigs with a total size of 4.98 Mb, and an N₅₀ contig length of 149.27 kb was submitted to GenBank.

The 72 contigs have a total size of 4,982,627 bp (with a G+C content of 41.92%) and were used for gene prediction and annotation by the RAST (Rapid Annotation using Subsystem Technology) system (1), with tRNAscan-SE-1.23 (3) software and RNAmmer1.2 (2) servers. Out of 4,282 genes predicted, 4,227 were predicted as coding regions (CDSs), 52 as tRNA, and 3 as rRNA genes. A comparison of the genome sequences available in the RAST server shows that Bacteroides sp. strain 2_1_7 (score, 530), Bacteroides sp. strain 3_1_19 (score, 501), and Parabacteroides distasonis ATCC 8503 (score, 491) were the closest neighbors of the strain JCM 21150^T.

Strain JCM 21150^T contains genes for the Entner-Doudoroff pathway, hyaluronidase (not present in Bacteroides sp. strain 2_1_7), 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45), 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16)/2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14), arylsulfatase (EC 3.1.6.1), beta-hexosaminidase (EC 3.2.1.52) (chitin and N-acetylglucosamine utilization), alpha-glucosidase (EC 3.2.1.20), beta-galactosidase (EC 3.2.1.23), N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28), ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92), dipeptidyl carboxypeptidase Dcp (EC 3.4.15.5), purine nucleoside phosphorylase (EC 2.4.2.1), aminoacyl-histidine dipeptidase (peptidase D) (EC 3.4.13.3), membrane-associated zinc metalloprotease, Xaa-Pro aminopeptidase (EC 3.4.11.9), and alpha-N-arabinofuranosidase (EC 3.2.1.55), involved in metabolism of biomacromolecules.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AJKI00000000. The version described in this paper is the first version, AJKI01000000.