Easy353: a tool to get Angiosperms353 genes for phylogenomic research

Z Zhang, P Xie, Y Guo, W Zhou, E Liu… - Molecular Biology and …, 2022 - academic.oup.com
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 …

[HTML][HTML] The sequenced angiosperm genomes and genome databases

F Chen, W Dong, J Zhang, X Guo, J Chen… - Frontiers in plant …, 2018 - frontiersin.org
Angiosperms, the flowering plants, provide the essential resources for human life, such as
food, energy, oxygen, and materials. They also promoted the evolution of human, animals …

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

WJ Baker, P Bailey, V Barber, A Barker… - Systematic …, 2022 - academic.oup.com
The tree of life is the fundamental biological roadmap for navigating the evolution and
properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering …

New targets acquired: Improving locus recovery from the Angiosperms353 probe set

TGB McLay, JL Birch, BF Gunn, W Ning… - Applications in plant …, 2021 - Wiley Online Library
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 …

Anchored phylogenomics of angiosperms I: assessing the robustness of phylogenetic estimates

C Buddenhagen, AR Lemmon, EM Lemmon, J Bruhl… - BioRxiv, 2016 - biorxiv.org
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 …

[HTML][HTML] PlantTribes2: Tools for comparative gene family analysis in plant genomics

EK Wafula, H Zhang, G Von Kuster… - Frontiers in Plant …, 2023 - frontiersin.org
Plant genome-scale resources are being generated at an increasing rate as sequencing
technologies continue to improve and raw data costs continue to fall; however, the cost of …

[HTML][HTML] aTRAM-automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

JM Allen, DI Huang, QC Cronk, KP Johnson - BMC bioinformatics, 2015 - Springer
Background Assembling genes from next-generation sequencing data is not only time
consuming but computationally difficult, particularly for taxa without a closely related …

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

R Ufimov, V Zeisek, S Píšová, WJ Baker… - Applications in Plant …, 2021 - Wiley Online Library
Premise Custom probe design for target enrichment in phylogenetics is tedious and often
hinders broader phylogenetic synthesis. The universal angiosperm probe set …

Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in …

BB Liu, ZY Ma, C Ren, RGJ Hodel… - … of Systematics and …, 2021 - Wiley Online Library
With the decreasing cost and availability of many newly developed bioinformatics pipelines,
next‐generation sequencing (NGS) has revolutionized plant systematics in recent years …

A new pipeline for removing paralogs in target enrichment data

W Zhou, J Soghigian, QY Xiang - Systematic Biology, 2022 - academic.oup.com
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing
method that has been increasingly used for phylogenomic studies. Unfortunately, current …