Draft Genome Sequence of the Novel Agar-Digesting Marine Bacterium HQM9

Abstract

Strain HQM9, an aerobic, rod-shaped marine bacterium from red algae, can produce agarases and liquefy solid plating media efficiently when agar is used as a coagulant. Here we report the draft genome sequence and the initial findings from a preliminary analysis of strain HQM9, which should be a novel species of Flavobacteriaceae.

GENOME ANNOUNCEMENT

Strain HQM9, which was isolated from the surfaces of red algae, is a yellow-pigmented, aerobic, Gram-negative, agar-degrading bacterium that represents a novel species in the family Flavobacteriaceae, based on its 16S rRNA gene sequence. The marine flavobacteria are known for producing enzymes that degrade polysaccharides such as agar, laminarin, xylan, fucoidan, and carrageenan from micro- or macroalgae (3, 5, 11, 13, 21). The agar-degrading bacteria play an important role in the marine carbon cycle involving the breakdown of agar and other sulfated galactans, which form a significant component of the cell walls of red and green algae, the egg jelly coating of certain sea urchin species, and the outer tunics of ascidians (2, 19). Over the past couple of years, the genome sequences of Flavobacteriaceaefamily members Flavobacterium psychrophilumJIP02/86 (8), Robiginitalea biformataHTCC2501 (17), Capnocytophaga ochraceaDSM 7271 (15), Zunongwangia profundaSM-A87 (20), and Gramella forsetiiKT0803 (4) have been published.

The genome of HQM9 was sequenced with a combined strategy of 454 genome sequencer FLX (454 GS FLX) sequencing and Illumina paired-end sequencing at the Beijing Institute of Genomics. The 454 GS FLX sequencing achieved about 21-fold coverage, and 498-fold coverage of reads was achieved by Illumina paired-end sequencing. The draft genome (about 4 Mbp) contains 183 contigs, which can be assembled into 74 scaffolds. Scaffold N50 is 440,279 bp. The GC content of the HQM9 draft genome is 33.2%. We predicted the tRNA genes by tRNAscan-SE (14). Ribosomal RNAs were found by BLAST searching against the Rfam database (10). Open reading frames (ORFs) were identified by using Glimmer 3.0 (7) and GeneMarkS (6). All predicted ORFs were then annotated by BLAST (1), InterPro (16), and KEGG.

The draft genome contains 3,971 protein-coding genes, 2 rRNA operons, and 37 tRNA genes. Three thousand five hundred nineteen predicted protein-coding genes have homologs in GenBank databases of nonredundant protein sequences (E value < 1e−5). Approximately 7% of HQM9 genes have similarity (identity of ≥30%) to those of Croceibacter atlanticusHTCC2559 (18), which also belongs to the Flavobacteriaceaefamily and for which the complete genome has been sequenced. Notably, 34 agarase genes, the most agarase genes detected in one bacterial genome so far, were found in the HQM9 draft genome. The agarases can be grouped into α-agarases and β-agarases according to the cleavage pattern presently known (9). The 34 agarases of HQM9 all belong to the β-agarase group, based on sequence similarity. Furthermore, the catalytic domains of β-agarases have been classified into three glycoside hydrolase (GH) families, i.e., GH-16, GH-50, and GH-86 (9). Of these 34 agarases, 14 belong to the GH-16 family, 6 belong to GH-86, and only 2 belong to GH-50 (http://www.cazy.org/glycoside-hydrolases.html). Agarase can catalyze the degradation of agarose polysaccharide into neoagaro-oligosaccharides by cleavage of the β-1,4 linkages (12, 22) and can help the bacterium get enough nutrients from the algae. Many other enzymes for degradation were also identified. Fifty-seven peptidases for digesting proteins and 14 glycoside hydrolases for digesting polysaccharides were predicted. According to the KEGG pathway analysis, most genes encode the HQM9 proteins for glycolysis, the citrate cycle (TCA cycle), the pentose phosphate pathway, galactose metabolism, and fatty acid metabolism. These metabolism pathways may provide enough energy to HQM9 for adapting to the complicated and changeable marine environment.

A more specific analysis of strain HQM9 will be reported in a future publication.

Nucleotide sequence accession number.

The draft genome sequence of HQM9 is available in GenBank under accession number AFPB00000000.