Draft genomes of Parafrankia sp. strains FMc2 and FMc6, isolated from root nodules of Morella cordifolia

TL;DR

This paper presents the draft genomes of two Parafrankia strains from root nodules of a specific plant species.

Contribution

The study provides new genomic data for two previously unstudied Parafrankia strains.

Findings

Strain FMc2 is closely related to Parafrankia strain Cc1.17.

Strain FMc6 belongs to the species Parafrankia soli.

Abstract

The genomes of two Parafrankia strains isolated from Morella cordifolia root nodules are described. Strain FMc2 is most closely related to Parafrankia strain Cc1.17, while FMc6 is a strain of Parafrankia soli.

Tables

TABLE 1. Parafrankia sp. genome information

Strain	Genome coverage	Number of scaffolds	N50 value (Kb)	Total length (bp)	GC (%)	Completenessa	Contaminationb
FMc2	32×	533	53.3	8,990,676	71.6	95.8%	1.29%
FMc6	17×	671	28.3	8,928,102	71.3	94.9%	0.83%

Full text

ANNOUNCEMENT

The family Frankiaceae contains free-living soil bacteria which form nitrogen-fixing symbiosis with actinorhizal plant hosts from eight families (1, 2). This symbiosis contributes to nitrogen reservoirs in terrestrial ecosystems and allows actinorhizal plants to perform as pioneers (3, 4). Taxonomic revision has expanded the number of genera within the family from one (Frankia) to four, containing strains from phylogenetic clusters 1, 2, 3, and 4 (5), broadly overlapping their associations with different host genera (1, 3, 4, 6). Morella represents more than half of the actinorhizal species in Africa (7, 8), forming effective symbioses with strains of both Frankia and Parafrankia (formerly Frankia clusters 1 and 3, respectively) (9). We describe genomes of two Parafrankia sp. strains isolated from Morella cordifolia (10, 11). Strains FMc2 and FMc6 were sequenced to provide information on Parafrankia diversity and selected from 10 strains isolated from African Morella (10, 11), based on 16S rRNA, 23S ITS rRNA, and nifH gene sequences, multilocus sequence analysis (MLSA), and phenotypic characterization (10–15). For all 10 isolates, partial sequences were deposited in GenBank under accession numbers KP342101-KP342110 (16S rRNA), KP342111-KP342120 (nifH), and KU174954-KU174963 (23S ITS rRNA). Gene fragments from MLSA were deposited under accession numbers KU174964-KU174973 (atpD), KU174974- KU174983 (dnaA), KU174984-KU174993 (ftsZ), KU174994-KU175003 (pgk), and KU175004-KU175013 (rpoB).

Parafrankia sp. strains FMc2 and FMc6 grew in the dark at 28°C in liquid defined propionate medium for 90 days and gDNA was extracted from single colonies using the CTAB method (16). Standard shotgun libraries were created using a Nextera XT DNA Library Prep kit and 3.0 Illumina chemistry (17). Sequencing was performed at the University of the Western Cape sequencing facility using an Illumina MiSeq platform (2 × 300 bp). For FMc2, sequencing generated 9,137,722 reads totaling 2,435 Mbp. For FMc6, sequencing generated 3,939,506 reads totaling 990 Mbp. Sequence reads were filtered and trimmed using fastp (18). Reads with an average %GC <54 were removed with BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/). Genomes were assembled using SPAdes 3.15.5 (19), and quality was assessed with BUSCO v5.7.1 (20) and CheckM v1.2.3 (21). Contigs shorter than 500 bp were discarded. Genome statistics were calculated using BBTools (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/), summary statistics are presented in Table 1. Default parameters were used unless stated otherwise.

Draft genomes were annotated via the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (22). Parafrankia sp. strain FMc2 contained 7,602 protein-encoding genes, 48 tRNAs, 2 complete rRNA regions, and 2 noncoding RNAs. Parafrankia sp. strain FMc6 contained 7,764 protein-encoding genes, 46 tRNAs, 2 complete rRNA regions, and 2 noncoding RNAs. The genome size and number of genes for both strains fall within the expected range for Parafrankia (5).

Whole-genome taxonomic analysis was performed via the Type Strain Genome Server (TYGS) platform (23), including digital DNA-DNA hybridization (dDDH) estimation in comparison to other Parafrankia genomes. Average nucleotide identity (ANI) was calculated using pyani v0.2.12 (24). Analyses included ten Parafrankia strains available from the NCBI genome database. Using a 70% dDDH species threshold, FMc6 was identified as a strain of Parafrankia soli (dDDH value 81.9%, ANI value 0.976), whereas FMc2 is most closely related to Parafrankia colletiae strain Cc1.17 (dDDH value 55.9%, ANI value 0.935). Bioinformatic analysis using antiSMASH (25) revealed abundant secondary metabolite biosynthetic gene clusters, as seen in other Parafrankia species (26, 27 ).