The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms

Abstract

Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods: We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result: The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search. Conclusion: The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.

Draft Genome Sequence of the Earthworm Eudrilus eugeniae

“…Also, the organs such as skin have a rich population of symbiotic microbes. We extracted the whole genome of Verminephrobacter eiseniae from the draft genome of E. fetida and published a paper [ 8 ]. Hence, we examined the hundreds of Gram-stained tissue sections of the prostate gland and checked them for the presence of any microbes.…”

“…The presence of 28 genes in purine metabolism and 19 genes in pyrimidine metabolism indicates the importance of the pathways. It has been reported that the symbiotic bacteria of Eisenia fetida was able to synthesize vitamin B2, thiamine, biotin, propionate, pyruvate, folate, and pantothenate and may provide to the worm [ 8 ]. In E. eugeniae, pathways for the metabolism of all these metabolites except propionate were observed.…”

“…The worm stages self-assemblage when introduced to the water together. The worms that have their heads cut off lose this social ability which they regain once the brain is formed [ 8 ]. This proves its potency as a model for studying mental disorders.…”

Stable expression ofHelicobacter pylori cagAoncoprotein in brinjal

“…The DNA fragments were purified from the agarose gel using the Genei clean purification technique (Genei Gel Extraction Kit). According to the instructions, the Miniprep Kit (Genei) has been used to obtain pure super-coiled plasmid DNA with excellent yield (35μl) (Arumugaperumal et al, 2020;Garcia Jr et al, 2020;.…”