Complete genome of Rhodovulum sp. HP10 isolated from the gastrointestinal tract of farmed shrimp

TL;DR

This paper presents the complete genome of a new Rhodovulum species isolated from farmed shrimp.

Contribution

The study provides the first complete genome sequence of Rhodovulum sp. HP10, a novel species.

Findings

The genome includes one chromosome and one plasmid with 4,128 coding sequences and 58 RNA genes.

Rhodovulum sp. HP10 represents a novel species based on genomic analysis.

Abstract

The complete genome sequence of Rhodovulum strain HP10, which was isolated from the gastrointestinal tract of whiteleg shrimp, is presented here. The bacterium has one chromosome (4.17 Mb), one plasmid (62.43 kb), 4,128 coding sequences (CDSs), and 58 RNA genes and represents a novel species.

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ANNOUNCEMENT

Rhodovulum is a genus of purple non-sulfur anoxygenic phototrophic bacterium belonging to the class Alphaproteobacteria. Previous studies have shown that several genera of purple non-sulfur bacteria are associated with the removal of chemical oxygen demand (COD), nitrogen compounds, and H_2_S (1–3). These bacteria also possess antibacterial properties, particularly the ability to inhibit pathogenic bacteria in shrimp, including Vibrio harveyi, Vibrio vulnificus, and Vibrio parahaemolyticus (4). Furthermore, Rhodovulum species are used as probiotics in shrimp aquaculture, contributing to the improvement of pond environment and shrimp health (5, 6).

Here, we announce the genome sequence of strain Rhodovulum sp. HP10. The strain was isolated from the gastrointestinal tract of whiteleg shrimp, collected from a shrimp pond in Hai Phong City, Vietnam. The genome sequencing of the strain Rhodovulum sp. HP10 was performed using single-molecule, real-time (SMRT) DNA sequencing technology on the PacBio platform. The quality control reads and de novo assembly were performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the long-read de novo assembler Flye version 2.9.5 (7). The contamination level of the assembled genome was assessed using the CheckM tool, which is integrated into the DDBJ Fast Annotation and Submission Tool web server (https://dfast.ddbj.nig.ac.jp/) (8). The quality and completeness of the assembled genome were evaluated using BUSCO version 5.8.0 (9). Annotation and gene prediction from the assembled genome were performed using the Rapid Annotations using Subsystems Technology (RAST) (10).

The complete genome consists of two contigs with a total length of 4,166,722 bp and a GC content of 67.19%. It has an N50 value of 4,104,297, an L50 of 1, and the largest contig length is 4,104,297 bp. The larger contig was identified as a chromosome, whereas the smaller contig was a plasmid with 62,425 bp in length. Genomic annotation reveals 4,186 genes, including 4,128 coding sequences (CDS) and 58 RNA genes. CheckM analysis indicates that the assembled genome has a completeness level of 99.3% and an estimated contamination of less than 1%.

To identify the taxonomy of strain Rhodovulum sp. HP10 and observe the relationships of the different species within the genus Rhodovulum, we conducted whole-genome-based taxonomic analyses with closely related type taxa using the Type Strain Genome Server (TYGS) (https://tygs.dsmz.de/) (11). Comparative analysis of digital DNA-DNA hybridization values between type strains of various Rhodovulum species and strain HP10 indicates that, with values below the 70% threshold, Rhodovulum sp. HP10 is a distinct species of the Rhodovulum genus.