mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data

Abstract

Next-generation sequencing is now a mature technology, allowing partial animal genomes to be produced for many clades. Though many software exist for genome assembly and annotation, a simple pipeline that allows researchers to input raw sequencing reads in fastq format and allow the retrieval of a completely assembled and annotated mitochondrial genome is still missing. mitoMaker 1.0 is a pipeline developed in python that implements (i) recursive de novo assembly of mitochondrial genomes using a set of increasing k-mers; (ii) search for the best matching result to a target mitogenome and; (iii) performs iterative reference-based strategies to optimize the assembly. After (iv) checking for circularization and (v) positioning tRNA-Phe at the beginning, (vi) geneChecker.py module performs a complete annotation of the mitochondrial genome and provides a GenBank formatted file as output.

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

“…Mitochondrial contigs were then identified by similarity search using blastn with e ‐value ≥ 1e−06 against our ant reference mitogenomic database. Each detected mitochondrial contig was then annotated with tblastx for protein‐coding genes (CDSs) and blastn for 16S and 12S rRNAs taking advantage of the geneChecker module of mitoMaker (Schomaker‐Bastos & Prosdocimi, 2018) that we incorporated into MitoFinder. Finally, we used arwen version 1.2 (Laslett & Canback, 2007) to detect and annotate tRNA genes.…”

Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano

“…number LT594767) as a reference to filter contigs containing mitochondrial sequences. The completion of the mitochondrial contigs was assessed using the script circularizationCheck.py (mito-Maker) 52 (script available from https ://githu b.com/RemiA llio/MitoF inder /blob/maste r/circu lariz ation Check .py) with contigs extended by mapping reads during several iteration steps in GENEIOUS 11.1.5 when needed 53 . The mitogenomes were annotated using MITOS2 webserver 54 and genes manually curated in GENEIOUS, particularly at 5′ and 3′ ends.…”

Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)

“…Mitochondrial contigs were filtered out using BLASTn ( e -value −30) against the mitogenome of H. lucifugax (GenBank accession number LT594767) as a reference. We assessed the completion of the mitochondrial contigs using the script circularizationCheck.py (mitoMaker) [ 36 ], and incomplete contigs were extended by iterative mapping of reads in GENEIOUS v11.1.5 [ 37 ]. The mitogenomes were annotated using MITOS2 [ 38 ] and genes manually curated in GENEIOUS, particularly at 5′ and 3′ ends.…”