Abstract
Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.
Highlights
Over time, mitochondrial genetics and genomics passed through a noticeable revolution in the process of data acquisition
The considerable simplicity in data acquisition has led evolutionary biologists to use mitochondrial multi-locus or complete mitogenome analyses to study phylogenetic relationships at different taxonomic levels thanks to: (i) improved resolution compared to single-locus analyses (i.e. Carapelli et al 2007); (ii) informativeness at different taxonomic levels due to the presence of genes characterized by dissimilar evolutionary rates, as well as the possibility to recode data as amino acids and according to the positioning of single genes; and (iii) availability of data from other species that can be readily included due to strict orthology of the mitochondrial genome across Metazoa
An error is displayed if: (i) the input archive is not prepared as required; (ii) input files are not in fasta format; (iii) duplicated sequence IDs are present within a file; (iv) non-IUPAC nucleotides are observed in a sequence; and v) stop codons are present within a sequence
Summary
Mitochondrial genetics and genomics passed through a noticeable revolution in the process of data acquisition. With the advent of next-generation sequencing (NGS) technologies, processing time and associated costs dropped, leading to a substantial increase in the rate of production, annotation, and publication of new mitochondrial genomes (i.e. 11,758 in January 2021 in the NCBI Organelle Database). The considerable simplicity in data acquisition has led evolutionary biologists to use mitochondrial multi-locus or complete mitogenome analyses to study phylogenetic relationships at different taxonomic levels thanks to: (i) improved resolution compared to single-locus analyses Given the increasing importance of mitogenomes for phylogenetic purposes, specialized journals (e.g. Mitochondrial DNA Part B Resources) were launched with the primary aim of publishing new mitochondrial DNA sequences to be used in phylomitogenomic analyses
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