Genome Sequence of the Thermostable-Agarase-Producing Marine Bacterium Catenovulum agarivorans YM01^T, Which Reveals the Presence of a Series of Agarase-Encoding Genes

Abstract

Marine bacterium Catenovulum agarivorans YM01^T can produce highly thermostable agarases. The draft genome of YM01^T is about 5.36 Mb and harbors approximately 4,913 genes, including 15 agarase (2 α-agarase and 13 β-agarase)-encoding genes, which will provide references to functional characterization of various agarases from marine bacteria.

GENOME ANNOUNCEMENT

The Gram-negative, rod-shaped, strictly aerobic, peritrichously flagellated, chain-forming, agar-hydrolyzing marine bacterium Catenovulum agarivorans YM01^T was recently isolated from seawater of the Yellow Sea in the coastal region of Qingdao, China, and was identified as a novel genus and species (5). Analysis of the 16S rRNA gene sequence revealed that the closest neighbors of YM01^T were the genera Glaciecola (88.4 to 91.0%), Colwellia (88.9 to 90.6%), Vibrio (88.9 to 90.4%), Aestuariibacter (89.3 to 90.4%), Bowmanella (90.1 to 90.3%), and Alteromonas (88.7 to 90.1%) in the class of Gammaproteobacteria. Further studies showed that YM01^T could produce thermostable agarases. After treatment at 100°C for 2 h, the crude extraction of agarases resulted in an agar-hydrolyzing capacity of 33.3% (data not shown). Thermostable agarase has various advantages over mesothermal agarase in industry applications. Here we report a draft genome sequence for C. agarivorans YM01^T for identification of thermostable-agarase-producing genes.

The Illumina HiSeq2000 sequencing approach with a 500-bp paired-end library was used for determining the C. agarivorans YM01^T genome, which achieved about 61.6-fold coverage. The reads were assembled using SOAPdenovo assembler software, and putative coding sequences (CDSs) were identified with Glimmer 3.0 (1). tRNA genes were directly predicted with tRNAscan-SE (2). Annotation was performed using the KEGG, COG, Swiss-Prot, TrEMBL, and NCBI nonredundant (NR) databases.

The draft genome of C. agarivorans YM01^T (about 4.87 Mb) contains 160 contigs, ranging from 59 bp to 216,200 bp (the N50 and N90 contig sizes are 82,176 bp and 20,773 bp, respectively), which can be assembled into 73 scaffolds ranging from 532 bp to 424,499 bp (N50 and N90 scaffold sizes are 212,606 bp and 59,093 bp, respectively). The G+C content was 40.04%. A total of 4,215 protein-encoding genes (89.85% among the whole genome) and 57 tRNA-containing genes were predicted in the draft genome. Among the predicted genes, 2,342 (55.6%) are assigned to COG categories (4) and 2,566 (60.9%), 2,074 (49.2%), 1,053 (25.0%), and 991 (23.5%) genes are found within the Swiss-Prot, KEGG, TrEMBL and NR databases, respectively.

More importantly, we identified 15 complete coding sequences for agarases (including 2 α-agarases and 13 β-agarases) from the C. agarivorans YM01^T genome, and they could be used for production of recombinant agar-degrading agarases for various commercial applications. Until now, only one complete genome sequence of an agar-degrading marine bacterium, Alteromonas sp. strain S89, which showed 89.0% 16S rRNA gene similarity to C. agarivorans YM01^T, has been reported (3), and the results of genome annotation identified 6 agarase-encoding genes. Finally, genome sequencing of C. agarivorans YM01^T provides references for functional characterization of various agarases from marine bacteria.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AJWM00000000. The version described in this paper is the first version, AJWM01000000.