Abstract
Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.
Highlights
With the onset of High Throughput Sequencing (HTS) technologies, we have entered an era in which massive nucleic acid sequencing is becoming routine in phylogenetic and biodiversity monitoring studies [1,2]
The results showed that MitoZ can recover 97.33% of protein coding genes (PCGs) and rRNA genes of the test samples, of which 94.66%
We investigated the influences of sequence characteristics on the assembly qualities, including mitochondrial derived reads (MDR) ratio, depth, A+T content and mitogenome heteroplasmy
Summary
With the onset of High Throughput Sequencing (HTS) technologies, we have entered an era in which massive nucleic acid sequencing is becoming routine in phylogenetic and biodiversity monitoring studies [1,2]. DNA extracts (e.g. environmental DNA (eDNA)), identify multiple taxa simultaneously from diverse types of samples – stomach contents [3], feces [4,5], sediments [6], soil or water [6,7,8]. In most cases, these studies deal with degraded DNA, are in urgent demand for short barcoding fragments for taxonomic identification [9,10]. In addition to its importance in biodiversity monitoring, mitochondrial genome records maternal inheritance information and is extensively utilized to infer phylogenetic relationship between diverse lineages [1,16]
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