Complete Genome Sequence of w Ana, the Wolbachia Endosymbiont of Drosophila ananassae

Abstract

Here, we present the complete genome sequence of the Wolbachia endosymbiont wAna, isolated from Drosophila ananassae and derived from Oxford Nanopore and Illumina sequencing. We anticipate that this will aid in Wolbachia comparative genomics and the assembly of D. ananassae specifically in regions containing extensive lateral gene transfer events.

Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement

“…Despite obtaining complete autosome and chromosome X arms, 10 the nuwts were assembled into nine contigs. Alignments between the 1.4 Mbp reference wAna Hawaii genome sequence (GenBank: CP042904.1) 11 and nuwt-containing D. ananassae contigs revealed the integration of an entire bacterial genome at least once, with most portions present at least twice and smaller portions present in three to ten copies (Figure 1A). Whole bacterial genome integration supports a DNA-based rather than an RNA-based mechanism of integration.…”

“…The Illumina library was sequenced on a HiSeq4000 instrument (Illumina). Illumina sequencing reads prepared from geographic strains of D. ananassae were obtained from SRA and described in Choi et al 7 Illumina sequencing reads prepared from the wAna Hawaii endosymbiont were obtained from SRA and described in Gasser et al 11 Total RNA was extracted from Wolbachia-cured and non-cured D. ananassae using the QIAzol lysis reagent (Qiagen). Whole flies were homogenized under liquid nitrogen in 1.5 mL tubes using a disposable pestle.…”

“…Of these, 41 genes (38,838 bp) were also present in the D. ananassae Hawaii nuwts as a single copy. Alignments containing wAna sequences from eight non-cured strains of D. ananassae with the cytoplasmic endosymbiont, 7,12 wAna integrations from cured D. ananassae Hawaii, and wAna endosymbiont sequences 11 were inspected for the presence of shared nucleotide differences in at least two sequences with respect to the Wolbachia endosymbiont of D. anomalata (wAno) as an outgroup. Shared differences were searched for in seven cured strains of D. ananassae by conducting BLASTN searches of the informative sites with 50 bp upstream/downstream (Table S5) against the corresponding SRA read database.…”

Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

“…To anchor contigs to chromosome 4, Dana.UMIGS contigs were aligned to caf1 assembly contigs previously assigned to chromosome 4 ( Leung et al 2017 ) using NUCmer ( Kurtz et al 2004 ) with -l 1000. Chromosome 4 contigs containing LGT from the fly’s Wolbachia endosymbiont ( w Ana) were anchored by aligning Dana.UMIGS contigs to the previously assembled w Ana genome ( Gasser et al 2019 ) with -l 1000. Alignments were filtered to retrieve the longest consistent set of alignments for each LGT contig.…”

Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements

“…If authors would like to submit a resource describing the genome of an organism that does not have a species designation, the authors can designate the organism as a member of an existing genus (e.g., Wolbachia sp. strain w Ana [ 2 ]) and note the organism’s similarity to, or difference from, its closest relative(s) using appropriate techniques and analyses that are fully described.…”