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

Arun Arumugaperumal,Sudhakar Sivasubramaniam,Saranya Lathakumari,Sayan Paul,Ravindran Balasubramani

doi:10.1186/s13213-020-01549-w

Arun Arumugaperumal, Sudhakar Sivasubramaniam + Show 3 more

Open Access

https://doi.org/10.1186/s13213-020-01549-w

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Abstract

PurposeVerminephrobacter 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.MethodsWe 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.ResultThe 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.ConclusionThe 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.

Highlights

The symbiosis has been recognized as a central driver for evolutionary innovation (Raina et al 2018)
The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu
The genome sequence assembly of V. eiseniae EF01-2 was used to fetch out the bacterial sequences from the genome dataset of raw reads sequences of earthworm Eisenia fetida (Figure S1)

Summary

Introduction

The symbiosis has been recognized as a central driver for evolutionary innovation (Raina et al 2018). The symbiotic relationship defines the interaction between the symbiont and host in an intimate association which can be mutualistic, commensalistic, or parasitic (Dimijian 2000) In mutualistic symbiosis, both the interacting partners get the benefit from each other. The bacterium, in turn, provides a reproductive advantage to the earthworm (Lund et al 2010; Viana et al 2018). Apart from this bacterial genus, there are other bacteria that harbor the earthworms’ nephridia (Davidson et al 2013). 191 16S rRNA genes of different Verminephrobacter clones are reported in the NCBI nucleotide database, and the whole genome of V. aporrectodeae At4 (T) and V. eiseniae EF01-2 was sequenced already (Kjeldsen et al 2012; Pinel et al 2008)

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