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Genome annotation. (XLSX 9 kb

Phylogenetic analysis of <i>Aethina tumida</i> Murray (Coleoptera: nitidulidae) from Reunion Island

The small hive beetle (SHB), Aethina tumida Murray, native to sub-Saharan Africa, is a parasite of Apis mellifera causing significant damage to honey bee colonies. For the past decades, it has spread to many countries worldwide and once established, eradication is difficult or not feasible. In July 2022, an outbreak was reported for the first time in a French department in the Indian Ocean, Reunion Island. The origin and the pathway of the introduction were not identified. The molecular characterisation of SHB specimens collected in the southern part of the island, where the beetle has infested several apiaries, was investigated in order to provide elements on the invasive source. The sequencing of the partial Cytochrome oxidase I gene from two specimens showed that they belonged to the same new haplotype. Phylogenetic analysis suggests an introduction either from an unidentified African source or from the Asian continent since the haplotype is similar to those characterized from China and Philippines.</p

Analysis software versions and parameter settings.

<p>* Unless otherwise specified, default parameters were used.</p

Analysis of the phylogenetic relationships of the <i>Wolbachia</i> nuclear insertions in the <i>Dictyocaulus viviparus</i> genome.

<p>Phylogenetic tree inferred from 16S rDNA, <i>groEL, ftsZ, dnaA</i> and <i>coxA</i> loci with maximum likelihood (RAxML) and Bayesian (MrBayes, PhyloBayes) inference. Branch support is reported as (RaxML/MrBayes/PhyloBayes). Strains representing <i>Wolbachia</i> supergroups A, B, C, D, F and H are indicated.</p

Relationships of nematode species harbouring <i>Wolbachia</i> symbionts.

<p>A phylogenetic cartoon showing the relationships of the nematode species discussed in this work <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004397#pgen.1004397-Blaxter1" target="_blank">[23]</a>. To the left, the systematic structure of the class Chromadoria is given, and the three major suborders within Rhabditida are highlighted. Lifecycle strategies of the groups are indicated. The fine-scale relationships of species discussed in the text are given to the right. The presence of live <i>Wolbachia</i> infection (+: yes, −: no), evidence of laterally-transferred <i>Wolbachia</i> sequences in the nuclear genome (+: yes, −: no, ?: unknown), and the availability of complete genome sequences (+: yes, −: no, ±: partial genome sequence) for each of the species are indicated.</p

Genome assembly and annotation metrics of <i>D. viviparus</i> and other Rhabditina species.

<p>Genome assembly and annotation metrics of <i>D. viviparus</i> and other Rhabditina species.</p

PCR test for <i>Wolbachia</i> insertions.

<p>* + strong positive band observed, and sequence confirmed; − no PCR product observed. All PCRs used New England BioLabs Phusion HF mix, an annealing temperature of 58 °C, 35 cycles of amplification, and were repeated twice with identical results.</p

Comparison of the <i>Dictyocaulus viviparus</i> proteome to that of other rhabditid nematodes.

<p>Venn diagram illustrating the orthoMCL clustering of the predicted proteome of <i>Dictyocaulus viviparus</i> (DVI) to those of <i>Caenorhabditis elegans</i> (CEL), <i>Heterorhabditis bacteriophora</i> (HBA) and <i>Haemonchus contortus</i> (HCO). The numbers of proteins clustered and the total number of predicted proteins is given below each species' name.</p

Matches to <i>Wolbachia</i> WO phage in the <i>Dictyocaulus viviparus</i> genome assembly.

<p>*Because the <i>Wolbachia</i> insertions in the <i>D. viviparus</i> genome were inactivated by mutation, many genes had multiple adjacent, independent high scoring segment matches in different frames in BLAST searches.</p

Comparison of <i>Wolbachia</i>-like insertions from two <i>Dictyocaulus viviparus</i> isolates, and relationships of the Cameroon <i>D. viviparous</i>.

<p>A. 16S rRNA gene fragments from the Cameroon isolate of <i>D. viviparus</i> (obtained through whole genome sequencing) and from the Moredun isolate (from specific amplification) are shown aligned. The genome sequence assembly has three copies of <i>Wolbachia</i>-like 16S genes, two tandemly arranged and truncated in scaffold scaf09320, and one in scaffold scaf01523. B. <i>ftsZ</i> gene fragments from the Cameroon isolate of <i>D. viviparus</i> (obtained through whole genome sequencing) and from the Moredun isolate (from specific amplification) are shown aligned. While we were able to amplify the complete fragment from the Moredun strain, the genome assembly contains only a truncated <i>ftsZ</i> gene (and no consensus is shown for the ∼200 bases of essentially unaligned sequence at the 5′ end of the alignment). C. Bayesian phylogenetic analysis of the complete nuclear small subunit ribosomal RNA (nSSU) genes of the Cameroon <i>D. viviparus</i> and other <i>Dictyocaulus</i> sp., and outgroups (taken from the European Nucleotide Archive). The Cameroon <i>D. viviparus</i> is most similar to the European <i>D. viviparus</i> sequenced previously. RAxML analyses yielded the same topology. The 5′ gene fragment isolated and sequenced from the Moredun strain was identical to the other <i>D. viviparus</i> nSSU sequences.</p