Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China.

Blastomonas is a strictly aerobic bacteriochlorophyll a-producing genus within the alpha-4 Proteobacteria. Here we report the first genome sequence from this genus. The draft genome of Blastomonas sp. strain AAP53 contains a split photosynthesis gene cluster and two gene clusters encoding a flagellar system. Genes for the autotrophic CO2 fixation pathway are absent.

GENOME ANNOUNCEMENT

The genus Blastomonas of the family Sphingomonadaceae (Alphaproteobacteria) is characterized by budding morphology and bacteriochlorophyll a synthesis under aerobic conditions. Only two type species have been reported in this genus, B. natatoria and B. ursincola (1–3). They are strictly aerobic chemoorganotrophs and facultative photoorganotrophs with motion ability by means of polar flagella. To assess the metabolic potentials and photosynthesis gene composition of Blastomonas species, we sequenced the whole genome of Blastomonas sp. strain AAP53. This yellow-pigmented isolate was collected in November 2011 from the surface water of the Swan Lake, a freshwater desert lake in the Inner Mongolia Autonomous Region, China.

Blastomonas sp. AAP53 was transferred five times on solid R2A media before inoculation into a liquid culture. DNA was extracted using a genomic DNA purification kit, and a 300-bp DNA library for Illumina sequencing technology was constructed. An Illumina HiSeq 2000 platform was employed for sequencing. Approximately 3.01 Gb raw data of 101-bp-long pair-end reads were generated. A total of 11,656,750 reads were subjected to quality control and trimming on the Galaxy server (4) and then were de novo assembled into contigs using the Velvet program (Ver. 1.2.08) (5). Various hash lengths between 31 and 91 were tested and an optimal assembly was achieved with a k-mer size of 57. Contigs less than 300 bp long were removed from the final assembly. Genome coverage was ca. 180×. Annotation was performed with the RAST (6) and BASys (7) servers.

The draft genome consisted of 28 contigs with an N50 value of 350,403 bp and a total length of 3.62 Mb, containing 3,369 open reading frames (ORFs) and 42 tRNAs. The G+C content was 63.6%. One complete rRNA operon was assembled. A full-length 16S rRNA gene sequence of this isolate shows 98.6% identity to that of Blastomonas natatoria strain DSM 3183. The photosynthesis gene cluster (PGC) was split and located on two separate contigs, probably due to insufficient sequencing coverage on the PGC region. A 13,758-bp-long contig contains the PGC genes of bchIDO-crtF-bchCXYZ-pufBALMC. Identified pufBALM protein sequences have 91 to 97% identity to those of B. natatoria and B. ursincola. A 55,061-bp-long contig contains the other part of PGC genes at its 3′ end, with a gene organization of puhE-acsF-ORF-puhCBA-lhaA-bchMLHBNF-ORF-ppsR-ORF-bchG-pucC-bchP-tspO-ORF.

Autotrophic CO2 fixation pathway genes are absent in this draft genome. There are genes encoding adenylyl-sulfate reductase, sulfite reductase, urea carboxylase, nitrite oxidoreductase, and nitrate reductase. Two gene clusters associated with the flagellar system were identified, with gene organizations of flaA-fliA-flhA-flgJ-ORF-flgMA-2×ORFs-flgBCDEFGHIJKL-motAB and fliSD-flhB-fliRQPONMLK-ORF-fliIHGFE. Various proteins that are involved in the aerobic respiratory electron transport chain were identified, including NADH dehydrogenase, cytochrome c oxidase, succinate dehydrogenase, and catalase, a finding that confirms the aerobic lifestyle of Blastomonas sp. AAP53. The presented genome sequences shall deepen our understanding of Blastomonas species and provide more insights into the metabolism and ecology of freshwater aerobic anoxygenic phototrophic (AAP) bacteria (8–11).

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ANFZ00000000. The version described in this paper is the first version, ANFZ01000000.