![]() ![]() Most metazoan mitochondrial genomes contain 37 genes, including 22 tRNAs, 13 protein-coding genes (PCGs), and two rRNAs. Furthermore, the characteristics of mtDNA enable the analysis of complex evolutionary processes such as gene rearrangements, replication, transcription, and regulation of gene expression at a resolution that is currently not possible for nuclear genomes. These features have made mitochondrial DNA (mtDNA) the most accessible genomic information for many species. Animal mitogenomes show very conserved genetic content, a limited occurrence of gene duplications, short intergenic segments, and generally lack introns. The metazoan mitochondrial genome consists of extranuclear DNA of relatively small size (16 to 20 kbp) that exists in a high copy number per animal cell. Metazoan mitogenomes are among the most abundant genomes deposited in nucleotide databases to date, with mitochondrial markers being selected as the most common DNA barcodes for species identification. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. biguttatus using High-Throughput Sequencing are presented. Two novel annotated mitogenome haplotypes for C. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. The best-performing mitogenome annotator was MITOS2. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. Among the utilized tools, BWA performed best for C. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. We observed performance differences between the compared mitogenome generation strategies. The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. All species present a high similarity in mitogenome organization. We also annotated or re-annotated the only available reference mitogenome for C. We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species. Generating novel mitogenomic information from single Culicoides sonorensis and C. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species. Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. ![]()
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