Draft Genome Sequence of the Anoxygenic Phototrophic Bacterium Rhodoferax sp. Strain U11-2br, Isolated from a Mountain Lake on the Ulagan Plateau

ABSTRACT We report the draft genome sequence of an anoxygenic phototrophic bacterium, Rhodoferax sp. strain U11-2br, which was isolated from a freshwater mountain lake on the Ulagan Plateau (Altai, Russia). The assembly contains 4,514,979 bp, with a GC content of 59.9%.

T he Ulagan Plateau is located in the south of Western Siberia. Research on the area has been mainly focused on paleoecology (1) and archaeology (2). Here, we present the first results of a microbiological study of the mountain lakes of the Ulagan Plateau.
Rhodoferax sp. strain U11-2br was isolated from a small (0.01-km 3 ) freshwater mountain lake (50°249320N, 87°359600E). The lake is surrounded by a mountain coniferous forest. At the time of sampling (July 2018), the water temperature was 12°C and the total mineralization was 0.098 g/liter (pH 8.44). A combined sample of sediment and water column was used to obtain an enrichment culture in the light. The U4 medium for the enrichment culture and subsequent agar shake dilutions contained the following: NaHCO 3 , 115 mg/liter of distilled water; KNO 3 , 0.5 mg/liter; Na 2 SO 4 , 6 mg/liter; NaCl, 1.5 mg/liter; K 2 HPO 4 , 10 mg/liter; sodium acetate, 500 mg/liter; the pH of the medium was adjusted to 8.5. Light-brown colonies composed of slightly curved motile rods were developed in an agar shake tube, and a pure culture was obtained by separating a single colony. The pure isolate was confirmed using optical microscopy and 16S rRNA gene sequencing, and it was designated Rhodoferax sp. strain U11-2br.
Genomic DNA was isolated from the cell culture using the QIAamp DNA minikit (Qiagen, Dusseldorf, Germany) following the manufacturer's recommendations. A pairedend DNA library (average insert size, 310 bp) was constructed using the Nextera XT DNA library preparation kit for Illumina (Illumina, USA). The DNA library was sequenced using an Illumina MiSeq system with 150-bp paired-end reads.
The draft genome sequence of Rhodoferax sp. strain U11-2br was constructed using the Shovill v. 1.1.0 pipeline (3), with read trimming using Trimmomatic v. 0.39 (4). Error correction of the Illumina reads was conducted using Lighter v. 1.1.2 (5). Overlapping and stitching of paired-end reads were completed with FLASH v. 1.2.11 (6). These reads were assembled de novo with SPAdes v. 3.14.1 (7). As a result, 78 contigs were assembled (N 50 , 108,245 bp). The draft genome sequence was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (8). The genome size is estimated to be 4,514,979 bp, with a GC content of 59.9%. Default parameters were used except where otherwise noted.
The sequenced genome was compared to the closest neighbors' genomes with the ChunLab online average nucleotide identity (ANI) calculator (https://www.ezbiocloud .net/tools/ani), which uses the OrthoANIu algorithm (9). ANI analyses confirmed discrepancies with the genomes of the closest neighbors.
The Rhodoferax sp. strain U11-2br genome has an ANI value of 75.64%, compared with the genome of Rhodoferax ferrireducens T118 (GenBank accession number GCA_000013605.1), with an average aligned length of 1,246,512 bp. The Rhodoferax sp. strain U11-2br genome has an ANI value of 93.55%, compared with the genome of Rhodoferax fermentans DSM 10138 (GenBank accession number GCA_016583655.1), with an average aligned length of 2,631,570 bp.

ACKNOWLEDGMENTS
The sampling was performed within the Institute for Water and Environmental Problems of the Siberian Branch of the Russian Academy of Sciences State Task framework (registration number 121031200178-8). The genome sequencing and analysis were supported by a Ministry of Science and Higher Education of the Russian Federation grant for the Kurchatov Center of Genome Research (agreement 075-15-2019-1659).