ABSTRACT
Dysgonomonas spp. are facultative heterotrophs which colonize diverse environments, including the hindgut of the lower termite Reticulitermes flavipes. Dysgonomonas genomes are enriched for genes involving oligo- and polysaccharide utilization, enabling modification of a wide array of complex glycans. Here, we report draft genome sequences for Dysgonomonas sp. strains BGC7 and HGC4.
ANNOUNCEMENT
Dysgonomonas spp. are facultative anaerobic heterotrophs which grow on many oligo- and polysaccharides. Dysgonomonas spp. are particularly prevalent in lignocellulolytic termites and cockroaches (reference 1 and references therein), and there is interest in understanding their metabolic potential, particularly with regard to the biotransformation of complex lignocellulose- and host-derived glycans (2). Here, we present draft genome sequences for Dysgonomonas sp. strains BGC7 and HGC4, cultured from the hindgut of the lower termite Reticulitermes flavipes.
Termite hindguts were extirpated using the technique described by Matson et al. (3). Strain BGC7 was isolated on modified Eggerth-Gagnon agar (ATCC medium, 2840), and strain HGC4 was isolated on the same medium, but sterile sheep blood was replaced with a hemin-vitamin K1 solution (25 mg and 5 mg ml−1, respectively). Cultures were maintained on rich peptone-hemin-glucose (rPHG) agar (1), and plates were grown anaerobically under an atmosphere of 89% N2, 5.5% CO2, and 5.5% H2 at 22°C. 16S rRNA gene sequences from isolates BGC7 and HGC4 (1) (available under GenBank accession numbers MT340878 and MT340881, respectively) placed both isolates within the genus Dysgonomonas. Genomic DNA was prepared using a Promega Wizard genomic DNA purification kit. Concentration and quality were determined by using gel electrophoresis and a Qubit fluorometer. DNA was mechanically sheared and Illumina TruSeq PCR-free libraries were prepared using DNA size selected for 550 bp. Libraries were sequenced on an Illumina MiSeq instrument using a 2 × 250-bp v2 kit. BBTools v36.38 (https://sourceforge.net/projects/bbmap/) was used to remove adapter sequences and quality trim and filter raw reads (threshold of Q15). Processed reads were assessed with FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and draft assemblies were created using A5-miseq v20160825 (4) and SPAdes v3.12.0 (5) using default settings on the KBase platform (6). Assemblies were merged using MAC (19 July 2020) (7) with default settings. Processed reads were aligned to MAC-merged assemblies using Bowtie 2 v2.3.2 (8), and SAMtools v1.10 (9) was used for file conversion. Pilon v1.23 (10) was used to polish merged assemblies iteratively three times. Polished assemblies were manually curated and annotated by submission to the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.13 (11). Genomes were checked for completeness and contamination using CheckM v1.0.18 (12) on KBase. Genomic relatedness to type and non-type strain Dysgonomonas genomes (available from RefSeq as of 15 October 2020) was determined by digital DNA-DNA hybridization (dDDH) performed using the Type Strain Genome Server (13). Average amino acid identities (AAI) between orthologous genes were computed with CompareM v0.1.1 (https://github.com/dparks1134/CompareM). Carbohydrate active enzyme (CAZy) domains were identified using the dbCAN2 server (14), and polysaccharide utilization loci (PULs) were identified using PULpy (15), with both using default settings.
Genome accession details, assembly metrics, phylogenetic relatedness, and CAZy/PUL content can be found in Table 1. The genomes of Dysgonomonas sp. strains BGC7 and HGC4 were enriched for CAZy domain-containing proteins and PULs involved in degradation of plant polysaccharides, particularly xylans. The availability of these sequences will contribute to understanding the metabolic potential and diversity of lignocellulose-degrading organisms, particularly within the genus Dysgonomonas.
Genome details of Dysgonomonas sp. strains
Data availability.Genome assemblies for isolates BGC7 and HGC4 were submitted to NCBI under BioProject accession number PRJNA656570 and whole-genome sequence (WGS) accession numbers JACMIC000000000.1 and JACMIB000000000.1, respectively. Detailed information can be found in Table 1.
ACKNOWLEDGMENTS
We thank Kendra Maas and the UConn Microbial Analysis, Resources, and Services (MARS) facility for consultation, Illumina library preparation, and sequencing.
This work was funded by the National Science Foundation Emerging Frontiers in Research and Innovation: Multicellular and Inter-Kingdom Signaling (EFRI-MIKS) award number 1137249 to Ranjan Srivastava, Leslie Shor, William E. Mustain, Kenneth Noll, J.G., and D.J.G. The funders had no role in data collection, interpretation, or preparation of data for publication.
FOOTNOTES
- Received 10 December 2020.
- Accepted 6 January 2021.
- Published 28 January 2021.
- Copyright © 2021 Bridges et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
