Draft Genome Sequences of Four Parasaccharibacter apium Strains Isolated from Honey Bees

ABSTRACT

Parasaccharibacter apium displays multiple ecological strategies in its honey bee host. We sequenced the genomes of four strains found in larvae and the adult gut in order to better understand its ecology and relationship to other Acetobacteraceae. The P. apium genome consists of 2,009,892 bp and 1,830 protein-coding genes.

GENOME ANNOUNCEMENT

Like many living things, honey bees live closely with a variety of microbes. The most studied example of honey bee-associated microbes are those that live in the honey bee worker gut, a microbiome that is composed of at least six core bacterial species clusters (1–6). The bacteria that live in the hive environment and outside the worker gut are less well understood (6–10). The newly described Parasaccharibacter apium is an acetic acid bacterium that occupies the hive but is rarely found in the adult worker gut (10, 11). Rather, P. apium is found in a wide variety of hive niches, including food stores, larvae, nurse worker crops and hypopharyngeal glands, worker jelly, and the queen gut (7, 9, 10, 12–14).

Three strains (A29, B8, and C6) of P. apium were isolated from honey bee larvae in the fall of 2013 (16S rRNA gene sequence accession numbers KM014158 [strain A29], KM014144 [strain B8], and KM014167 [strain C6] [10]). One “hindgut” strain (G7_7_3c) was also isolated from an adult forager ileum as part of another survey (16S rRNA gene sequence accession number KF600354 [9]). Total DNA was extracted from each isolate and was subjected to whole-genome shotgun sequencing. Paired-end reads (300 bp) were generated using the Illumina MiSeq platform at MR DNA (Shallowater, TX) and V3 chemistry.

The initial de novo genome assemblies of each strain were performed using MIRA version 4.0.2 (15). The data were randomly subsampled to approximately 75× coverage, and all (including high- and low-quality) reads were used for the assembly according to Chevreux et al. (16). Contigs less than 500 bp were excluded from further analysis. Contigs were ordered by mapping the assembled contigs to the genome of Saccharibacter sp. strain AM169 in MAUVE (17). The quality of the assembly was evaluated using QUAST with no reference genome (18) and the default parameters.

For the four strains, the assembly resulted in an average ± standard error (SE) of 29 (minimum, 26; maximum, 34) contigs, 2,009,892 ± 619 bp, an N₅₀ value of 182,699 ± 14,225 bp, and a G+C content of 59% ± 0.01%. The annotation was performed in Rapid Annotations using Subsystems Technology (19), which predicted 1,830 ± 12 protein-coding sequences and 1 rRNA.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers LMYH00000000 (strain A29), LMYI00000000 (strain B8), LMYJ00000000 (strain C6), and CP020554 (hindgut strain G7_7_3c).