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Classification of the UBCF_13 COG based on COG database in NCBI

Citation

Fatiah, Raudhatul et al. (2021), Classification of the UBCF_13 COG based on COG database in NCBI, Dryad, Dataset, https://doi.org/10.5061/dryad.sn02v6x4g

Abstract

Background: The Serratia plymuthica UBCF_13 is a phylloplane associated plant bacterium showing antifungal activity. Whole genome sequence provides information to get more insight about evolutionary study, unique traits in the genome and possibility to explore potential of this microorganism for future study. Here, we report the genome sequence of S. plymuthica UBCF_13 and the comparison with other seventeen strain.

Methods: Continuous short reads were attained from Illumina sequencing runs and reads of 150 bp were merged into a single dataset. A pan-genome based method was used to identify the core-genome of S. plymuthica species and the unique gene in UBCF-13.

Results: Assembled Illumina reads of S. plymuthica strain UBCF_13 genome was produced a 5.46 Mb circular genome sequence. 3315 genes were found to belong to the core-genome sheared by the 18 strains evaluated. The UBCF_13 genome harbors 488 unique genes, where 300 of which only can be found in this strain. The raw and assembled data is available via NCBI Short Read Archive (accession Number: SRR15012717) and genome database (accession number: CP068771).

Methods

Translated protein coding genes of UBCF_13 was used to identification of cluster of orthologous groups (COG). It was obtained by NCBI BLAST+rpsblast (Galaxy Version 2.10.1+galaxy0) and eggNOG Mapper (Galaxy Version 2.0.1+galaxy1) (eggNOG, RRID:SCR_002456). The result of COG assignment was classified based on categories in COG database NCBI.