Abstract
Bacillus sp. strain HYC-10 was isolated with intestinal tract content of a fish, Mugil cephalus, captured from the sea close to Xiamen Island, China. Here, we present the draft genome of strain HYC-10, which contains 3,611,918 bp with a G+C content of 41.30% and contains 3,687 protein-coding genes and 33 tRNA genes.
GENOME ANNOUNCEMENT
The genus Bacillus was first proposed by Cohn (1) and contains 260 type strains (http://www.bacterio.cict.fr/b/bacillus.html). Bacteria of this genus are important probiotics. Bacillus sp. strain HYC-10 (MCCC 1A00008) was isolated from intestinal tract content of a marine fish, Mugil cephalus, captured from the sea close to Xiamen Island, China. It showed the highest 16S rRNA gene similarity to Bacillus stratosphericus strain 41KF2aT (99.9%). Five type strains of the genus Bacillus (B. stratosphericus 41KF2a, Bacillus aerophilus 28K, Bacillus altitudinis 41KF2b, Bacillus safensis DSM 19292, and Bacillus pumilus DSM 27) shared high 16S rRNA gene sequence similarity (>99.0%) (2). Up to now, 78 strains of this group were isolated from various marine environments in our lab (http://www.mccc.org.cn).
The genome sequence of Bacillus sp. HYC-10 was determined by Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China), using Solexa paired-end sequencing technology. A total of 9,884,474 paired-end reads (500-bp library) were generated to reach a 443-fold depth of coverage with Illumina/Solexa Genome Analyzer IIx (Illumina, San Diego, CA), and the gaps among scaffolds were closed by custom primer walks or by PCR amplification followed by DNA sequencing. The genome of Bacillus sp. HYC-10 consists of 134 contigs (>200 bp; N90 = 70) of 3,611,918 bp and had an average G+C content of 41.30%. Automatic gene annotation was carried out by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html), followed by manual editing. The genome contains 3,687 candidate protein-encoding genes (with an average size of 855 bp), giving a coding intensity of 87.3%. A total of 2,446 proteins were assigned to cluster of orthologous groups (COG) families (4). Thirty-three tRNA genes for 18 amino acids (lacking Lys and Pro) were identified. The proteins associated with transcription (K; 276 open reading frames [ORFs]; 11.3%) were the most abundant group of COG, followed by the ones associated with amino acid transport and metabolisms (E; 261 ORFs; 10.6%) and inorganic ion transport and metabolism (P; 204 ORFs; 8.3%).
Up to now, three genomes of the Bacillus pumilus group, including Bacillus pumilus ATCC 7061T, Bacillus pumilus SAFR-032 (1a), and Bacillus pumilus S-1 (3), were released. Their genome size and GC content were similar to those of strain HYC-10 (ranging from 3.1 Mb to 3.8 Mb and from 41.3 mol% to 41.7 mol%, respectively). The genome sequence of strain HYC-10 and its curated annotation are important assets to better understand the physiology and metabolic potential of B. pumilus group-related species and will open up new opportunities to understand its function in fish intestinal tract content.
Nucleotide sequence accession number.
The draft genome sequence of Bacillus sp. HYC-10 has been deposited in GenBank under accession number AMSH00000000 (chromosome).
ACKNOWLEDGMENTS
We acknowledge Qiang Li and his colleagues for genome analysis at Shanghai Majorbio Bio-pharm Technology Co., Ltd.
This work was financially supported by the Public Welfare Project of SOA (201005032) and the International Science and Technology Cooperation Program of China (2010DFB23320).
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