First draft genome sequence of a member of the genus planomicrobium, isolated from the chandra river, India.

We report the first draft genome sequence of a member of the genus Planomicrobium, isolated from a soil sample from the Chandra River, located in the cold deserts of Himachal Pradesh, India. The draft genome assembly for Planomicrobium glaciei strain CHR43 has a size of 3,900,800 bp with a G+C content of 46.97%.

GENOME ANNOUNCEMENT

The genus Planomicrobium is composed of aerobic, motile, Gram-positive to Gram-variable rod- to coccus-shaped bacterial strains. So far, nine species of the genus Planomicrobium have been defined, viz., P. koreense, P. okeanokoites, P. mcmeekinii, P. alkanoclasticum, P. psychrophilum, P. chinense. P. glaciei, P. stackebrandtii, and P. flavidum. Members of the genus Planomicrobium have been isolated from fermented seafood, marine mud, Antarctic samples, intertidal sediments, and glacier and marine solar salterns (1). However, a genome sequence for any species of the genus Planomicrobium had not yet been determined. The psychrotolerant bacterium Planomicrobium glaciei CHR43 was isolated from a soil sample from the Chandra River (latitude 32°24′55″, longitude 77°14′06″), located in a cold desert area of the Lahaul and Spiti district, Himachal Pradesh, India. The genome of P. glaciei CHR43 was sequenced, given the organism's ability to grow and produce protease enzyme over a wide range of temperatures (5 to 42°C). The whole-genome shotgun sequencing of P. glaciei CHR43 was performed using the Illumina Genome Analyzer IIx in the 76-bp paired-read format. A total of 73,533,050 raw reads were obtained with 5,588,511,800 bp of raw sequence. To obtain the high-quality (HQ) data, reads were filtered using NGS QC toolkit v 2.3 (2) (cutoff read length for HQ, 70%; cutoff quality score, 20). A total of 57,816,970 (78.63% raw reads) adaptor/primer free reads were used for de novo genome assembly using Abyss v 1.3.4 (3). In the data set, the k parameters (from 29 to 71) were optimized for best assembly, and at 68mers, 82% (23,717,433) of the reads were found to be paired and 14.7% (4,252,610) of the reads were singletons. The final assembly contains 103 contigs with a total size of 3,900,800 bp, an N50 contig length of 66,943 nucleotides (nt), the longest contig length of 442,487 nt, and a G+C content of 46.97%. The annotation was performed with the help of the RAST (Rapid Annotation using Subsystem Technology) server using the Glimmer 3 option (4), which predicted 3,934 coding genes, 76 RNA genes, and 406 predicted SEED subsystem features.

A comparison of the CHR43 genome sequence with existing genome sequences, performed using the RAST server, revealed that Lysinibacillus sphaericus C3-41 (score 521) and Bacillus sp. strain B-14905 (score 495) are its closest neighbors. The genome analysis of P. glaciei showed that all the genes for the Embden-Meyerhof pathway (glycolysis) were present. The presence of a gene for the enzyme methylglyoxal synthase, which allows the bacterium to bypass the lower part of glycolysis in carbon-rich but phosphorus-limited conditions, is an indication that P. glaciei prefers glycolytic substrates (5). P. glaciei also has all the enzymes for the pentose phosphate pathway. In P. glaciei, genes for enzymes for the utilization of fructose, galactose, mannitol, sucrose, ribose, trehalose, d-mannose, and lactose were also present. In addition, genes encoding peptidase/protease (93 genes), lipase (13 genes), and cold shock proteins (5 genes) were found.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AUYR00000000. The version described in this paper is first version, AUYR01000000.