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Gene presence absence in Serratia plymuthica strains

Citation

Fatiah, Raudhatul et al. (2021), Gene presence absence in Serratia plymuthica strains, Dryad, Dataset, https://doi.org/10.5061/dryad.1zcrjdfsj

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 strains.

Methods: A pan-genome based method was used to identify the core-genome and the the gene presence or absence in of the S. plymuthica strains

Results: The pan-genome idenfied the gene presence and absence in the S. plymuthica strains. The total genes was 10455. Comparative genomics analysis revealed 3.315 core proteins/ genes shared among 18 strains. The genome of the UBCF_13 harbors 488 unique genes, of which 300 genes are only contained by this strain.

Methods

Comparative genomics analysis was carried out using genome sequences of UBCF_13 from this research and 17 whole sequenced genomes of other Serratia plymuthica strains retrieved from NCBI’s GenBank. The genomes were reannotated using Prokaryotic genome annotation (Prokka, Galaxy Version 1.14.6+galaxy0) (Prokka, RRID:SCR_014732). Identification of genes shared between the strains, and presence-absence gene set were carried out using Roary ((Galaxy Version 3.13.0+galaxy1) (Roary, RRID:SCR_018172) with minimum percentage identity for blastp was 70%.