Computational protocol: Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila strain KOR1, Isolated from a Mangrove Plant (Kandelia obovata)

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Protocol publication

[…] There has been increased interest in quorum sensing (e.g., N-acylhomoserine lactone [AHL] molecules) to evaluate the interactions between microbes and mangrove plants (). In the rhizosphere environment, previous studies have shown that root-associated bacterial isolates produce AHLs and exhibit various functions, including facilitating nitrogen fixation (), promoting plant growth (), stimulating primary root elongation (), and resisting pathogens (). Recently, we isolated Aeromonas hydrophila KOR1 (a nitrogen-fixing bacterium) from Kandelia obovata, and found that it can secrete short-chain (C4–C6) AHL molecules. Although the phenotype was observed, this type of functionality has not yet been elucidated at the genomic level. Moreover, no genome data of this strain from a wetland environment have been reported. Here, we performed whole-genome sequencing of this bacterium and searched for its AHL-encoding gene.The genomic DNA of A. hydrophila KOR1 was extracted using the DNA extraction kit (MoBio, USA) according to the manufacturer’s instructions. The whole-genome shotgun project of A. hydrophila KOR1 was performed using pair-end sequencing in an Illumina MiSeq sequencing platform (Illumina, USA), which was performed by Shenzhen Hengchuan Gene-Tech. Co., Ltd. The reads were assembled with SOAPdenovo version 2.04 (), and the sequence was annotated using the RAST annotation server (). tRNA and rRNA genes were predicted by tRNAscan-SE () and RNAmmer (), respectively. Genes were predicted using Glimmer version 3.02 () and were annotated by searching against the NCBI-NR and KEGG databases.The whole genome comprised 5 scaffolds consisting of 14 contigs with a total length of 4,783,170 bp. The G+C content was 61.82%. From the draft genome sequence, a total of 4,249 genes were identified in the genome with an average length of 956 bp. Homologous comparison by BLAST found 2,833 coding sequences involving 22 functional COG groups and a portion of the coding sequences involving 34 metabolic pathway KEGG groups. A total of 149 noncoding RNAs were found in the genome, including 113 tRNAs, 30 rRNAs, and 6 sRNAs.Based on the functional categories of COG (http://www.ncbi.nlm.nih.gov/COG), 180 genes were found to be related to signal transport and interaction processing. Potentially, these genes are key features of A. hydrophila KOR1 that enable it to release or receive all kinds of signals, including biological and chemical information. With respect to AHL signals, the AHL-encoding gene (LuxR) was predicted to be located at contig 8, with a length of 623 bp. In addition, a putative autoinducer-2 production protein LuxS gene was also found. The whole-genome analysis revealed the presence of a quorum-sensing encoding gene (LuxR), which is crucial for understanding the A. hydrophila KOR1 AHL-dependent phenotypes and their ecological function in the rhizosphere environment. […]

Pipeline specifications

Software tools SOAPdenovo, RAST, tRNAscan-SE, RNAmmer, Glimmer
Databases KEGG
Applications Genome annotation, WGS analysis
Organisms Aeromonas hydrophila