Targeted NGS for species level phylogenomics : "made to measure'' or "one size fits all''?
Date
2017
Journal Title
Journal ISSN
Volume Title
Publisher
PeerJ
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising
source of data for inferring multiple, meaningfully resolved, independent gene trees
suitable to address challenging phylogenetic problems in species complexes and rapid
radiations. The targets in question can either be adopted directly from more or less
universal tools, or custom made for particular clades at considerably greater effort.
We applied custom made scripts to select sets of homologous sequence markers from
transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae).
We compared the resulting targets to those that would be selected both using different
available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of
more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent
genomes (including MarkerMiner, irrespective of input data) delivered fewer and
shorter potential markers than those targeted for Erica. The latter may nevertheless be
effective for sequence capture across the wider family Ericaceae. We tested the targets
delivered by our scripts by obtaining an empirical dataset. The resulting sequence
variation was lower than that of standard nuclear ribosomal markers (that in Erica
fail to deliver a well resolved gene tree), confirming the importance of maximising the
lengths of individual markers. We conclude that rather than searching for "one size fits
all'' universal markers, we should improve and make more accessible the tools necessary
for developing "made to measure'' ones.
Description
CITATION: Kadlec, M., et al. 2017. Targeted NGS for species level phylogenomics : "made to measure'' or "one size fits all''?. PeerJ, 5:e3569, doi:10.7717/peerj.3569.
The original publication is available at https://peerj.com
The original publication is available at https://peerj.com
Keywords
Bioinformatics, Evolutionary studies, Plant science, Ericaceae, Hybridization enrichment
Citation
Kadlec, M., et al. 2017. Targeted NGS for species level phylogenomics : "made to measure'' or "one size fits all''?. PeerJ, 5:e3569, doi:10.7717/peerj.3569