nrDNA:mtDNA copy number ratios as a comparative metric for evolutionary and conservation genetics

Heredity
William Paul Goodall-Copestake

Abstract

Identifying genetic cues of functional relevance is key to understanding the drivers of evolution and increasingly important for the conservation of biodiversity. This study introduces nuclear ribosomal DNA (nrDNA) to mitochondrial DNA (mtDNA) copy number ratios as a metric with which to screen for this functional genetic variation prior to more extensive omics analyses. To illustrate the metric, quantitative PCR was used to estimate nrDNA (18S) to mtDNA (16S) copy number ratios in muscle tissue from samples of two zooplankton species: Salpa thompsoni caught near Elephant Island (Southern Ocean) and S. fusiformis sampled off Gough Island (South Atlantic). Average 18S:16S ratios in these samples were 9:1 and 3:1, respectively. nrDNA 45S arrays and mitochondrial genomes were then deep sequenced to uncover the sources of intra-individual genetic variation underlying these 18S:16S copy number differences. The deep sequencing profiles obtained were consistent with genetic changes resulting from adaptive processes, including an expansion of nrDNA and damage to mtDNA in S. thompsoni, potentially in response to the polar environment. Beyond this example from zooplankton, nrDNA:mtDNA copy number ratios offer a promising metric to help i...Continue Reading

References

Jul 1, 1966·Proceedings of the National Academy of Sciences of the United States of America·I B Dawid
Jun 1, 1968·Proceedings of the National Academy of Sciences of the United States of America·J G Gall
Apr 3, 2003·Genome Génome / Conseil National De Recherches Canada·Cheryl D ProkopowichTeresa J Crease
Jun 12, 2004·Biological Reviews of the Cambridge Philosophical Society·Helga Guderley
Sep 18, 2012·Molecular Phylogenetics and Evolution·Matthias BerntPeter F Stadler
Oct 11, 2012·PloS One·Ryuji J Machida, Nancy Knowlton
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
May 3, 2013·Cold Spring Harbor Perspectives in Biology·Mikhail AlexeyevSusan LeDoux
Jan 7, 2014·Biochimica Et Biophysica Acta·Justin HallgrenMichal Hetman
May 23, 2014·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Yue LiQing-Peng Kong
Jan 30, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Charlotte CaptSophie Breton
Mar 5, 2015·Heredity·D PorcelliR R Snook
Dec 8, 2015·Neurobiology of Aging·Angela PyleGavin Hudson
Feb 24, 2016·ELife·Ed ReznikChris Sander
Mar 13, 2016·BMC Bioinformatics·Melanie SchirmerChristopher Quince
Mar 16, 2016·PLoS Genetics·Manja WachsmuthMark Stoneking
Sep 29, 2018·F1000Research·Steven W Wingett, Simon Andrews

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Datasets Mentioned

BETA
LC333178-LC333181

Methods Mentioned

BETA
PCR

Software Mentioned

Oligo Analysis Tool
FastQC
PCRmax Eco Study
Geneious
Geneious mapper

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