Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi)

The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons.

oxygenic bacterium of the family Chloroflexaceae of the phylum Chloroflexi. Strain MS-G was isolated from a phototrophic microbial mat in an effluent channel of Mushroom Spring, an alkaline siliceous hot spring in the Lower Geyser Basin of Yellowstone National Park (44°32=20.4Љ N, 110°47=52.8Љ W, WY, USA). The 16S rRNA sequence of this isolate shares Ͼ99% nucleotide identity to a 16S rRNA sequence obtained from the metagenome (IMG taxon OID 3300002510) of the green upper layer (upper 1 mm), and both share 100% with the most abundant Chloroflexus sp. ITAG sequence (253 bp) of the microbial mat at 60°C. The 16S rRNA sequence was 98% similar to cultured isolates Chloroflexus spp. strains 396-1 and NPE (EMBL acc. nos. AJ308498 and AJ308502 [1]), and Յ94% identical to that of the type strains Chloroflexus aurantiacus J-10-fl T and C. aggregans DSM 9485 T .
Purified genomic DNA of Chloroflexus sp. strain MS-G was sequenced using an Illumina MiSeq instrument. The draft genome was assembled with Newbler (version 2.9, Roche) from 2,715,946 paired end reads with a minimum length of 301 bp into 263 contigs. For genome analysis contigs without any predicted ORFs were excluded leading to an assembly of 251 contigs with a minimum length of 500 bp, comprising 4,784,183 bp with an average GϩC-content of 55% and median coverage of 262-fold.
Annotation using RAST (2) predicted 4,064 protein coding genes and 49 tRNA-encoding genes, which is the same number of tRNA genes found in the C. aurantiacus strain J-10-fl T genome (3). Based on coverage, three rRNA operons with identical 16S rRNA and slightly different 23S rRNA gene sequences are predicted. Phyla-AMPHORA (4) identified all 198 Chloroflexispecific phylogenetic marker genes, which suggested that the draft genome is nearly complete and that the genome is comparable in size to those of other phototrophic Chloroflexi species (4.7 to

Mb [3]). Based on gene content and physiological studies, strain MS-G is an oxygen-tolerant anoxygenic phototroph.
Genes encoding type-2 (quinone-type) photosynthetic reaction centers (pufLM), and light-harvesting complex 1 (pufAB) as well as chlorosome proteins are present to enable phototrophic growth. The draft genome includes genes encoding all enzymes required for the synthesis of bacteriochlorophylls a and c, the presence of which was verified by high-performance liquid chromatography. A complete set of genes for the enzymes of the 3-hydroxypropionate cycle indicates the potential for autotrophic growth, which was observed in agar-shakes using sulfidecontaining growth medium with bicarbonate and CO 2 as the sole carbon sources in repeated transfers. The carotenoid biosynthesis pathway in strain MS-G is probably similar to that in other Chloroflexus spp., which produce ␥-carotene, ␤-carotene, echinenone, 1=-OH-␥-carotene, and the glucoside and glucoside esters of 1=-OH-␥-carotene (5). Consistent with the production of these carotenoids, the MS-G genome contains phytoene synthase (crtB), homologs of phytoene saturases and desaturases (crtI, crtD), lycopene cyclase (crtY), a 1=, 2=hydratase (cruF), 1=-OHglycosyltransferase (cruC), carotenoid glycoside acyltransferase (cruD), and beta-carotene 4-ketolase (crtO) (6,7).
Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JPIM00000000. The version described in this paper is version JPIM01000000.