Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Premise Custom probe design for target enrichment in phylogenetics is tedious and often
hinders broader phylogenetic synthesis. The universal angiosperm probe set …
hinders broader phylogenetic synthesis. The universal angiosperm probe set …
New targets acquired: Improving locus recovery from the Angiosperms353 probe set
PREMISE Universal target enrichment kits maximize utility across wide evolutionary breadth
while minimizing the number of baits required to create a cost‐efficient kit. The …
while minimizing the number of baits required to create a cost‐efficient kit. The …
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data
R Ufimov, JM Gorospe, T Fér… - Molecular Ecology …, 2022 - Wiley Online Library
The analysis of target enrichment data in phylogenetics lacks optimization toward using
paralogues for phylogenetic reconstruction. We developed a novel approach of detecting …
paralogues for phylogenetic reconstruction. We developed a novel approach of detecting …
A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining
DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the …
DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the …
A hybrid capture RNA bait set for resolving genetic and evolutionary relationships in angiosperms from deep phylogeny to intraspecific lineage hybridization
M Waycott, K van Dijk, E Biffin - BioRxiv, 2021 - biorxiv.org
Novel multi-gene targeted capture probes have been developed with the objective of
obtaining multi-locus high quality sequence reads across any angiosperm lineage. Using …
obtaining multi-locus high quality sequence reads across any angiosperm lineage. Using …
Easy353: A tool to get Angiosperms353 genes for phylogenomic research
The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear
genes that were selected by examining more than 600 angiosperm species. These genes …
genes that were selected by examining more than 600 angiosperm species. These genes …
A new pipeline for removing paralogs in target enrichment data
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing
method that has been increasingly used for phylogenomic studies. Unfortunately, current …
method that has been increasingly used for phylogenomic studies. Unfortunately, current …
On the potential of Angiosperms353 for population genomic studies
M Slimp, LD Williams, H Hale… - Applications in Plant …, 2021 - Wiley Online Library
PREMISE The successful application of universal targeted sequencing markers, such as
those developed for the Angiosperms353 probe set, within populations could reduce or …
those developed for the Angiosperms353 probe set, within populations could reduce or …
The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions
KP Hendriks, T Mandáková, NM Hay… - Applications in Plant …, 2021 - Wiley Online Library
Premise Researchers adopting target‐enrichment approaches often struggle with the
decision of whether to use universal or lineage‐specific probe sets. To circumvent this …
decision of whether to use universal or lineage‐specific probe sets. To circumvent this …
Anchored phylogenomics of angiosperms I: assessing the robustness of phylogenetic estimates
An important goal of the angiosperm systematics community has been to develop a shared
approach to molecular data collection, such that phylogenomic data sets from different focal …
approach to molecular data collection, such that phylogenomic data sets from different focal …