The genome of the Hepatincola symbiont of A. vulgare was sequenced from a female isopod collected from a natural population in Availles-Thouarsais, France (46° 51’ 37” N, 0° 8’ 28” E) in 2014. Hepatincola was known to be present in this population from our previous metabarcoding study [33 (link)]. DNA was extracted from both pairs of midgut glands using phenol-chloroform extraction. In total, 4.5 µg of DNA were used for size selection using AMPure XP beads (Beckman Coulter, USA) at a bead:sample ratio of 0.7x to enrich in long fragments. In total, 3.5 µg of DNA were recovered and used for library preparation using the Oxford Nanopore Ligation Sequencing kit SQK-LSK 108 (Oxford Nanopore Technologies, UK). The library was sequenced on an R9.4 flowcell on the MinION sequencer for 58 h. The run was stopped and restarted several times to optimize pore use. Basecalling was done using Albacore v2.0.1 using a quality threshold of Q7. After discarding low quality (A. vulgare (Accession: GCA_004104545.1) using Minimap2 v2.15 [38 (link)], resulting in 1,083,710 reads. The reads ≥1 kb were assembled using Canu v1.7 [39 (link)], producing a 1.37 Mbp circular contig containing two 16S rRNA genes 99% identical to the 16S rRNA gene sequence of Hepatincola from P. scaber (Accession: AY188585). This initial assembly was first polished with Nanopore reads using Nanopolish v0.11.1 [40 (link)] and subsequently with Illumina reads using Racon v1.4.3 [41 (link)]. Additional Illumina polishing with Polypolish v0.4.3 [42 (link)] did not detect additional errors. Illumina reads mapping onto the Hepatincola genome were extracted from A. vulgare shotgun metagenomic datasets from our previous study [43 (link)], in which DNA from different tissues (including the midgut glands) of the same Hepatincola-infected individual had been included.
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