Computational protocol: Genome Sequence of Photobacterium halotolerans MELD1, with Mercury Reductase (merA), Isolated from Phragmites australis

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Protocol publication

[…] Photobacterium spp. are Gram-negative bacteria belonging to the family Vibrionaceae. Though they are found to be primarily associated with marine environments (), Photobacterium halotolerans MELD1 was isolated from the rhizosphere of a terrestrial weed, Phragmites australis, found growing in mercury- and dioxin-contaminated land located near the seacoast (). In our previous study, we demonstrated that P. halotolerans MELD1 helped with the phytoprotection of Vigna unguiculata from mercury stress (). To gain insight into the genetic traits among the closely related P. halotolerans strains, whole-genome sequencing of terrestrial environment dwelling P. halotolerans MELD1 was performed.The MELD1 whole-genome sequence was obtained using Illumina technology. Ten micrograms of total DNA was sonicated by a Misonix 3000 sonicator to sizes ranging from 400 to 500 bp. DNA sizing was checked by a bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara). One-microgram sonicated DNA was end repaired, A tailed, and adaptor ligated following Illumina’s Trueseq DNA preparation protocol. The sequences generated went through a filtering process to obtain the qualified reads. ConDeTri () was implemented to trim or remove the reads according to the quality score. Cleaned and filtered nuclear reads were assembled de novo using ABySS (). Genome annotations were created in MAKER 2.00 () using a GeneMark () model trained for MELD1 via self-training. The resulting predictions were searched against the NCBI nonredundant (nr) database by using BLASTp.The whole-genome draft of P. halotolerans MELD1 consists of 57 contigs for a total of 4,758,037 bp with an overall G+C content of 51%, 258 pseudogenes, 17 rRNA genes, and 88 tRNA genes. In our previous work, we identified the presence of a merA gene and its mercury reductase activity, as well as resistance to toxic compounds like cadmium, lead, and dioxin (). As a trait of adaptation to the mercury-contaminated habitat, the genome of MELD1 contains a mer operon containing a mercury reductase gene (merA). Furthermore, MELD1 had a cluster of genes responsible for stress resistance, multidrug efflux pumps, and aerobactin siderophore. They also bear lux genes and genes responsible for gamma aminobutyric acid (GABA) () and pyrroloquinoline quinone (PQQ) (). These unique characteristics make the strain P. halotolerans MELD1 an effective plant growth-promoting bacterium in heavy metal-contaminated environments. […]

Pipeline specifications

Software tools ConDeTri, ABySS, GeneMark, BLASTP
Applications Genome annotation, WGS analysis
Organisms Phragmites australis
Chemicals Mercury