Computational protocol: Whole genome sequencing of Halomonas sp. SUBG004 isolated from Little Rann of Kutch, a desert of India

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Protocol publication

[…] Halomonas sp. strain SUBG004 is a Gram negative, rod-shaped bacterium isolated from the saline desert soil of Little Rann of Kutch in Gujarat, India. The isolate was acquired by culture-plating on 10% w/v NaCl containing nutrient rich medium and then its capacity to survive in M9 minimal medium with 10% w/v NaCl was explored. Here we report the complete genome of Halomonas sp. SUBG004.Genomic DNA was extracted from 12 hour old culture using protocol . Sequencing of the Halomonas sp. SUBG004 genome was performed by the Ion Torrent Technologies and raw reads were assembled by MIRA v. 2014. A total of 1982 contigs with an accumulated length of 4,897,364 bp (50.0X coverage) were annotated by GeneMarkS + method. The genome contains 93 tRNA genes and 44 rRNA genes as predicted using tRNAscan 1.2 and RNAmmer 1.2 , respectively, results enlisted in .Coding sequences were functionally annotated by Rapid Annotation using the Subsystems Technology (RAST) server in 451 subsystems (). Gene sequences of a betaine synthesis operon putatively encoding BetI: HTH type transcriptional regulator, BetA:Choline dehydrogenase (EC 1.1.99.1) and BetB:Betaine aldehyde dehydrogenase (EC 1.2.18) were identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database available in RAST . […]

Pipeline specifications

Software tools GeneMarkS, tRNAscan-SE, RNAmmer, RAST
Databases KEGG
Application Genome annotation