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BMC Evol Biol
2018 May 30;181:80. doi: 10.1186/s12862-018-1198-x.
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Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids.
Bronstein O
,
Kroh A
,
Haring E
.
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BACKGROUND: In 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.
RESULTS: Here 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.
CONCLUSIONS: Our 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.
Fig. 1. Representation of echinoid complete mitochondrial genomes assembled from NGS data, showing gene annotation and coverage. The annotated genomes are represented by four echinoid species: Hemicentrotus pulcherrimus, Strongylocentrotus fragilis, Mesocentrotus franciscanus, and Strongylocentrotus intermedius, corresponding to GenBank accession numbers: KC898202, KC898198, KC898199, and KC898200, respectively. Annotations are given at the outer margin of the external circle. Concentric circles represent the corresponding coverage for each of the represented species mitogenomes. Data was obtained from Kober and Bernardi [86, 87]. Enlarged segment illustrates the position of the various primers used in the current study. Coverage was calculated in BRIG [88], after read mapping with Bowtie2 [89] (using the predefined alignment threshold “very-sensitiveâ€). Annotations are based on those for H. pulcherrimus (GenBank accession no. NC_023771) and radial plots generated using BRIG
Fig. 2. Pairwise tree comparisons for phylogenetic trees based on commonly used mitochondrial markers. Trees include the two most commonly used phylogenetic mitochondrial markers: a fragment of the cytochrome c oxidase subunit 1 (a) gene and a fragment of the 16S ribosomal RNA (c) as well as the novel tRNAs and control region (e). To facilitate independent comparisons, the genetically inferred trees were restricted to the 35 publicly available complete echinoid mitochondrial genomes. Genera represented by more than one species were collapsed and are depicted by single branches. Supporting values (> 0.85 posterior probabilities and > 75% ML bootstrap values) are shown next to nodes. Topological comparisons between the genetically inferred trees and current classification (b, d, f) (see text for details) were visualised using Phylo.io [62]. Colour scale for the comparison metric (a variant of the Jaccard Index as implemented in Phylo.io) ranges from 0 (subtrees completely different) to 1 (subtree structure of the respective node is identical)
Fig. 3. Substitution saturation plot of the CRA marker based on the CRA-All dataset. The number of transitions (s) and transversions (v) is plotted against F84 genetic distance. A linear correlation is sustained for both transitions and transversions as expected in the absence of saturation
Fig. 4. Phylogenetic tree reconstruction of the echinoid control region and adjacent areas (CRA). The BI tree presented is based on 86 unique haplotypes retrieved from a total of 110 sequences, 405 bp long (see Table 1 for details on the sequences used for this tree). Supporting values (> 0.5 posterior probabilities and > 50% ML bootstrap values) are shown above the nodes
Alikhan,
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
2011,
Pubmed
Aquadro,
Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals.
1983,
Pubmed
Barker,
Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene.
2012,
Pubmed
Bensch,
Mitochondrial genomic rearrangements in songbirds.
2000,
Pubmed
Bjourson,
Band-stab PCR: a simple technique for the purification of individual PCR products.
1992,
Pubmed
Bouhlal,
Twin Mitochondrial Sequence Analysis.
2013,
Pubmed
Boyko,
Complex population structure in African village dogs and its implications for inferring dog domestication history.
2009,
Pubmed
Brandon,
MITOMAP: a human mitochondrial genome database--2004 update.
2005,
Pubmed
Bribiesca-Contreras,
Identification of echinoderms (Echinodermata) from an anchialine cave in Cozumel Island, Mexico, using DNA barcodes.
2013,
Pubmed
,
Echinobase
Bronstein,
Cryptic speciation in pan-tropical sea urchins: a case study of an edge-of-range population of Tripneustes from the Kermadec Islands.
2017,
Pubmed
,
Echinobase
Bronstein,
The taxonomy and phylogeny of Echinometra (Camarodonta: Echinometridae) from the red sea and western Indian Ocean.
2013,
Pubmed
,
Echinobase
Bronstein,
Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids.
2018,
Pubmed
Bronstein,
Do genes lie? Mitochondrial capture masks the Red Sea collector urchin's true identity (Echinodermata: Echinoidea: Tripneustes).
2016,
Pubmed
,
Echinobase
Brown,
Rapid evolution of animal mitochondrial DNA.
1979,
Pubmed
Cadahía,
Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae.
2009,
Pubmed
Cantatore,
The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.
1989,
Pubmed
,
Echinobase
Capella-Gutiérrez,
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
2009,
Pubmed
De Giorgi,
Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome.
1996,
Pubmed
,
Echinobase
Diniz,
The hypervariable domain of the mitochondrial control region in Atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring.
2005,
Pubmed
Eberhard,
Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona.
2001,
Pubmed
Ekblom,
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.
2014,
Pubmed
Felsenstein,
DISTANCE METHODS FOR INFERRING PHYLOGENIES: A JUSTIFICATION.
1984,
Pubmed
Gan,
Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes.
2014,
Pubmed
Ghatak,
Polymorphism in mtDNA control region of Mizo-Mongloid Breast Cancer samples as revealed by PCR-RFLP analysis.
2016,
Pubmed
Goodwin,
Coming of age: ten years of next-generation sequencing technologies.
2016,
Pubmed
Hoareau,
Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata.
2010,
Pubmed
,
Echinobase
Huang,
Characterization and evolution of the mitochondrial DNA control region in Ranidae and their phylogenetic relationship.
2016,
Pubmed
Huerta-Cepas,
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.
2016,
Pubmed
Irwin,
Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples.
2009,
Pubmed
Jacobs,
Sea urchin egg mitochondrial DNA contains a short displacement loop (D-loop) in the replication origin region.
1989,
Pubmed
,
Echinobase
Jacobs,
Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.
1988,
Pubmed
,
Echinobase
Jeffery,
Phylogeny and evolution of developmental mode in temnopleurid echinoids.
2003,
Pubmed
,
Echinobase
Jiang,
Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships.
2011,
Pubmed
Kasamatsu,
A novel closed-circular mitochondrial DNA with properties of a replicating intermediate.
1971,
Pubmed
Katoh,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
2013,
Pubmed
King,
High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq.
2014,
Pubmed
Kober,
Phylogenomics of strongylocentrotid sea urchins.
2013,
Pubmed
,
Echinobase
Kober,
Erratum to: Phylogenomics of strongylocentrotid sea urchins.
2017,
Pubmed
,
Echinobase
Kryukov,
Deep Phylogeographic Breaks in Magpie Pica pica Across the Holarctic: Concordance with Bioacoustics and Phenotypes.
2017,
Pubmed
Lanfear,
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.
2017,
Pubmed
Langmead,
Fast gapped-read alignment with Bowtie 2.
2012,
Pubmed
Larsson,
AliView: a fast and lightweight alignment viewer and editor for large datasets.
2014,
Pubmed
Littlewood,
A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata).
1995,
Pubmed
,
Echinobase
Liu,
Comparison of next-generation sequencing systems.
2012,
Pubmed
Ludwig,
Heteroplasmy in the mtDNA control region of sturgeon (Acipenser, Huso and Scaphirhynchus).
2000,
Pubmed
Marcet-Houben,
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.
2011,
Pubmed
McElhoe,
Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq.
2014,
Pubmed
McMillan,
Rapid rate of control-region evolution in Pacific butterflyfishes (Chaetodontidae).
1997,
Pubmed
Peng,
Characterization of the complete mitochondrial genome of Bombyx huttoni (Lepidoptera: Bombycidae).
2016,
Pubmed
Pereira,
Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region.
2008,
Pubmed
Rech,
Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus.
2014,
Pubmed
Robinson,
Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.
2016,
Pubmed
Ronquist,
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
2012,
Pubmed
Sanger,
DNA sequencing with chain-terminating inhibitors.
1977,
Pubmed
Shao,
Evolution of duplicate control regions in the mitochondrial genomes of metazoa: a case study with Australasian Ixodes ticks.
2005,
Pubmed
Singh,
Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes.
2008,
Pubmed
Smith,
Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).
2006,
Pubmed
,
Echinobase
Stoneking,
Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes.
1991,
Pubmed
Walberg,
Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA.
1981,
Pubmed
Wang,
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions.
2011,
Pubmed
Ward,
DNA barcoding discriminates echinoderm species.
2008,
Pubmed
,
Echinobase
Warren,
RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses.
2017,
Pubmed
Wu,
Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida.
2017,
Pubmed
Xia,
An index of substitution saturation and its application.
2003,
Pubmed
Xia,
The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes.
1998,
Pubmed
Xia,
DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution.
2017,
Pubmed
Zhang,
Genetic diversity of mitochondrial control region (D-Loop) polymorphisms in Coilia ectenes taihuensis inhabiting Taihu Lake, China.
2017,
Pubmed
Zigler,
Speciation on the coasts of the new world: phylogeography and the evolution of bindin in the sea urchin genus Lytechinus.
2004,
Pubmed
,
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