Practical considerations for plant phylogenomics

Abstract

The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project‐dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up‐and‐coming technologies that may help propel the field even further.

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

“…Genomic targeted enrichment approaches have been shown to be more efficient and economic than Sanger sequencing (Lemmon & Lemmon, 2013; McKain et al, 2018) and have been widely used in phylogenetic studies in recent years (Xi et al, 2014; Fisher et al, 2016; Hart et al, 2016; Mitchell et al, 2017; Couvreur et al, 2018). In this study, we targeted nuclear genes as they have been suggested to hold the greatest potential for investigating the evolutionary history of angiosperms for several reasons.…”

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

“…Genomic targets of hybridization‐based enrichment approaches can be recovered using “universal” baits optimized across broad taxon sets (e.g., the Angiosperm v.1 kit of Buddenhagen et al., ; the Angiosperms‐353 probe set of Johnson et al., ; the fern bait kit of Wolf et al., ) and using “taxon‐specific” baits designed for a focus group, ranging in taxonomic scale from populations (e.g., Euphorbia balsamifera Aiton; Villaverde et al., ) to a variety of higher‐level taxa (e.g., Inga Mill., Nicholls et al., ; Asclepiadoideae, Weitemier et al., ; Asteraceae, Mandel et al., ). The increasing availability of public transcriptome data and pipelines for LSCN gene discovery and bait development that require relatively few genomic resources can enable clade‐specific bait design, making phylogenomic research in groups of interest more attainable (see McKain et al., for details).…”

Methods for exploring the plant tree of life

“…Although hybrid enrichment is certainly one popular method of producing libraries for sequencing, McKain et al (2018) and genome skimming. They also offer guidelines for researchers to determine which approaches may be appropriate for their specific study.…”

“…Although hybrid enrichment is certainly one popular method of producing libraries for sequencing, McKain et al. () provide an overview of the growing options for phylogenomic studies, including microfluidic PCR, RAD‐seq, target enrichment, transcriptomes, and genome skimming. They also offer guidelines for researchers to determine which approaches may be appropriate for their specific study.…”