Genome of Serratia plymuthica UBCF_13, Insight into diverse unique traits

Genomic DNA isolation and sequencing

S. plymuthica strain UBCF_13 was isolated from phylloplane of Brassica juncea L. in 2012 from District of Solok, Province of West Sumatera, Indonesia¹⁰. The bacterium was cultivated in Luria–Bertani (LB) broth at 27°C for 16 hours with 150 rpm. The genomic DNA was extracted using the method of Chen and Kuo (1993)¹¹, followed by degrading residual RNA by RNAse. Library preparation and sequencing was done by Novogen (Hong Kong). Sequencing was performed using Illumina NovaSeq 6000 (Illumina NovaSeq 6000 Sequencing System, RRID:SCR_016387).

Genome assembly and annotation

Continuous short reads of 150 bp were merged into a single dataset. The dataset was obtained by using combination of map-based gene references and de novo assembly that was performed in Geneious software (Geneious, RRID:SCR_010519)¹². The annotation in genome submission was carried out using NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAP)¹³. The annotated genome sequence of UBCF_13 has been deposited in the NCBI GenBank under accession number CP068771.

Comparative genomics of Serratia plymuthica strains

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 the Prokka software tool (Prokka, Galaxy Version 1.14.6+galaxy0) (Prokka, RRID:SCR_014732)^14,15 that is available from the NCBI. Identification of genes shared between the strains, and ‘presence-absence gene set’ was carried out using Roary; Galaxy Version 3.13.0+galaxy1, (Roary, RRID:SCR_018172)¹⁶ with a threshold similarity of 70%.

Genes that exist in all the strains are the core-genome. Phylogenetic trees were constructed using Maximum Likelihood based inference of large phylogenetic trees-RAxML, Galaxy Version 8.2.4+galaxy2 (RAxML, RRID:SCR_006086)¹⁷ based on multialignment of concatenate core-genome. Phandango (Phandango, RRID:SCR_015243)¹⁸ was used to view the resulted output graphs.

Cluster of the orthologous groups of UBCF_13

The translated protein coding genes of UBCF_13 was used for identification of cluster of orthologous groups (COG). This was obtained from NCBI BLAST+rpsblast (Galaxy Version 2.10.1+galaxy0)¹⁹ and eggNOG Mapper (Galaxy Version 2.0.1+galaxy1) (eggNOG, RRID:SCR_002456)²⁰. The result of COG identification was classified based on the categories in COG database NCBI²¹.

Comparative genomics of Serratia plymuthica strains

The whole genome sequencing reads of Serratia plymuthica UBCF_13 were assembled into a single circular 5.46 Mb chromosome with overall GC content of 56.2% (Table 1). S. plymuthica has a genome size in the range 5.40–5.70 Mb. The GC content percentage is 55.70–56.60. Based on genome reannotation by Prokka, it was found different number of CDS in each genome S. plymuthica (Table 1). All of the compared S. plymuthica genomes shared a highly conserved genomic architecture as inferred from synteny of protein coding orthologs.

Figure 1A shows the phylogenetic tree of 18 strains S. plymuthica. The phylogenetic tree shows that S. plymuthica UBCF_13 is in same cluster with strain AS9, PRI-2C, NCTC8015, and NCTC8900. The strain PRI-2C is reclassified and transferred to the species S. inhibens²². The pangenome was performed together with other strains in order to obtain further insight into specific features in the UBCF_13. It was found 3315 belong to the core-genome shared by the 18 strains evaluated. The genome of the UBCF_13 harbors 488 unique genes, of which 300 genes are only contained by this strain. The presence-absence gene set was shown in file supplementary data 1

Figure 1. Maximum Likelihood tree and visualization of comparative genomic (pan genomic) between 18 strain S. plymuthica.

(a) Phylogenetic of 18 strains S. plymuthica based on concatenate core-genome multialignment; and (b) visualization of presence (blue bar)-absence (white bar) gene in each of the strains.

The Cluster of Orthologous Groups of UBCF_13

Functional categories of the CDS in S. plymuthica UBCF_13 based on the Cluster of Orthologous Groups (COG) categories are shown in Table 2. The list of UBCF_13 COG and its function classification based on COG database was shown in extended dataset 2²³.

Extended data

Dataset 1:

Dryad: Gene presence absence in Serratia plymuthica strains. https://doi.org/10.5061/dryad.1zcrjdfsj²⁴

This project contains the following extended data;

Dataset 2:

Dryad: Classification of the UBCF_13 COG based on COG database in NCBI https://doi.org/10.5061/dryad.sn02v6x4g²³

This project contains the following extended data;

Data are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).