Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

Abstract

BackgroundIn Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription.While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region.ResultsHere we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids.ConclusionsOur target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1198-x) contains supplementary material, which is available to authorized users.

A phylogenomic resolution of the sea urchin tree of life

“…These arguments have since been rejected by nearly every phylogenetic analysis [9,10,12,25,[29][30][31][60][61][62]; the strong support in our phylogenomic analysis for the monophyly of the sampled irregular echinoids is therefore largely uncontroversial. Although our taxonomic sampling is insufficient to establish which clade constitutes the sister group to Irregularia, we do not recover diadematoids or pedinoids in such a position, as previously suggested [12,37]. Instead, our topology shows Echinacea as their closest relative among the sampled taxa (as in [25], among others).…”

“…Nextgeneration sequencing (NGS) efforts have been applied to relatively small phylogenetic questions, concerned with the resolution of the relationships within Strongylocentrotidae Gregory, 1900 [34], a clade of model organisms, as well as among their closest relatives [35]. Although several studies have attempted to use molecular data to resolve the backbone of the sea urchin phylogeny [8,10,25,30,36,37], all these have relied on just one to three genes, usually those encoding ribosomal RNA. The lack of comprehensive sampling of loci across the genome thus limits the robustness of these phylogenies.…”

The Complete Mitochondrial Genome of The American Palm Cixiid, Haplaxius Crudus (Hemiptera: Cixiidae)

“…Hemipteran insects from the suborders Fulgoromorpha, Coleorrhyncha and Heteroptera are typically AC skewed [42]. The control region in the H. crudus mitochondrial genome corresponds to the control region of vertebrate mitogenomes and contains the origin sites for transcription and replication [48]. In the H. crudus mitochondrial genome, 18 noncoding regions ranging from 1 to 1,210 bp were observed in addition to the control region.…”

The Detection and Partial Localisation of Heteroplasmic Mutations in the Mitochondrial Genome of Patients with Diabetic Retinopathy

“…Several pathogenic mutations have been identified in genes encoding tRNAs located within the region encompassed by amplicon P, namely, tRNA phenylalanine [24], proline [25], threonine [26], and glutamic acid [27]. The control region is a hypervariable region of noncoding DNA which has been used to trace human population lineages [28]. Mutations in this region have been identified in several cancers [29][30][31].…”