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

BMC Evolutionary Biology
Omri BronsteinElisabeth Haring

Abstract

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. Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic...Continue Reading

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Citations

Jan 31, 2019·Molecular Plant-microbe Interactions : MPMI·Kegui ChenVincent N Fondong
Dec 14, 2018·BMC Evolutionary Biology·Nicolás Mongiardino KochGreg W Rouse
Dec 15, 2019·International Journal of Molecular Sciences·Afshan N MalikSobha Sivaprasad
Oct 8, 2020·Molecular Biology and Evolution·Zheng Bin Randolph QuekDanwei Huang
Dec 29, 2020·IUBMB Life·Ana Victoria Lechuga-ViecoJosé Antonio Enríquez
Apr 30, 2021·Genome Biology·Giulio FormentiUNKNOWN Vertebrate Genomes Project Consortium
Jul 31, 2021·PloS One·Paulo Eduardo T SoaresDaniel Carlos F Lanza

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Datasets Mentioned

BETA
SRR835993

Methods Mentioned

BETA
PCR

Software Mentioned

DAMBE6
trimAl
Bowtie2
CRA
io
MAFFT
Phylo
treeKO
RWTY package
Python Environment for Tree Exploration ( ETE )

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