Encarsia agona mitogenome

Encarsia agona mitogenome assembly and annotation

Whole genome sequence data from the Illumina MiSeq sequencer from three E. agona individuals imported into Geneious 8.1.9 for mitochondrial genome (mitogenome) assembly using the Geneious Mapper program (see below). Mitogenome assembly of the holotype E. agona using HTS platform-derived sequences was first attempted using Megaphragma viggianii (originally published as the misidentified amalphitanum Viggiani, GenBank KT 373787, Nedoluzhko et al. 2016; Polaszek et al. 2022) as the mitochondrial DNA genome template, it being the only chalcidoid mitochondrial DNA genome publicly available at the time. Assemblies of the holotype and paratype specimens’ mitogenomes carried out using Geneious v. 8.1.9, with the initial assembly involving three iterations at the ‘ sensitivity/Fast’ sensitivity settings and without sequence trimming. Gene fragments representing partial mtDNA coding sequence regions (CDS) were identified from this initial assembly. These agona mtDNA gene regions were used as subsequent partial species-specific reference DNA templates build up the mitogenome of the E. agona holotype. All regions from different versions of the holotype E. agona mtDNA genome were visually inspected for contig assembly quality.

Poorly assembled regions such as between intergenic regions were reassembled by introducing gap lengths (inserting between 50–100 Ns) followed by reassembling using the sensitivity detailed above. This process of quality checks/gap insertion/reassembling was repeated until no overlapping ambiguity of assembled intergenic regions was detected. This process enabled sequence fragments representing overlapping intergenic regions to be identified and to be into a high-quality contig. For post-assembly mitogenome annotation, we used the MITOS program ( Bernt et al. 2013), specifying genetic code 5 (invertebrate mitochondrial) with visualisation manual fine-tuning of the annotated mitogenomes in Geneious v. 8.1.9.