Identifying genetic markers for a range of phylogenetic utility-From species to family level

PloS One
Bokyung ChoiCarsten Külheim

Abstract

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the...Continue Reading

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Citations

Aug 3, 2021·Applications in Plant Sciences·Todd G B McLayChris J Jackson

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Methods Mentioned

BETA
Restriction-site Associated DNA Sequencing
RNAseq
electrophoresis
Assay
PCR

Software Mentioned

Aliscore
EPS
RAxML
MAFFT
SeaView
BLASTN
IQ
Flexbar
Geneious
SeqCap EZ System

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