Mitogenome sequence accuracy using different elucidation methods

Abstract

Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

“…Indeed, sequencing strategies and/or annotation methodologies can influence the results in terms of length of the mitogenome sequence recovered or in the gene length [ 69 ]. Some studies have documented the presence of dissimilarities in the assembly and annotation of mitochondrial genomes that are not always associated with low coverage [ 69 , 70 ].…”

“…Indeed, sequencing strategies and/or annotation methodologies can influence the results in terms of length of the mitogenome sequence recovered or in the gene length [ 69 ]. Some studies have documented the presence of dissimilarities in the assembly and annotation of mitochondrial genomes that are not always associated with low coverage [ 69 , 70 ]. In addition, not all the species are necessarily sensitive to this problem, which complicates the identification of a uniform approach to obtaining reliable mitochondrial genomes [ 69 ].…”

“…Some studies have documented the presence of dissimilarities in the assembly and annotation of mitochondrial genomes that are not always associated with low coverage [ 69 , 70 ]. In addition, not all the species are necessarily sensitive to this problem, which complicates the identification of a uniform approach to obtaining reliable mitochondrial genomes [ 69 ]. Since gene order is not affected by the methodology used, our results can be reasonably considered not to be an artefact.…”

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

“…We corrected several start codon positions in nad genes which have very variable 5′ ends, following the methodology described hereunder. The quality of mitogenome data is influenced by, amongst others, the raw sequence quality, the sequence assembly and the annotation methods 46 . We therefore suggest that authors report the main criteria they used to annotate mitogenome data deposited in GenBank, as we do here.…”

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

“…In addition, both software can only generate mitogenome assembly as their final outputs. Thus, separate software, like DOGMA (29), MOSAS (30), MITOS (31) are required for the following genome annotation (32). Besides, all of the three aforementioned annotation software only provide web page version and can hardly deal with assembly with multiple scaffolds.…”