Practical considerations for plant phylogenomics

• Published in: Applications in plant sciences Vol. 6; no. 3; pp. e1038 - n/a
• Main Authors: McKain, Michael R., Johnson, Matthew G., Uribe‐Convers, Simon, Eaton, Deren, Yang, Ya
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.03.2018; John Wiley and Sons Inc
• Subjects: Data analysis; Datasets; Deoxyribonucleic acid; DNA; Enzymes; Evolution; genome skimming; Genomes; herbaria; Hybridization; Library collections; microfluidics; Nucleotide sequence; Phylogenetics; phylogenomics; Plant sciences; Polyploidy; RAD‐seq; Review; sequence capture; Success; transcriptomes; United States > US; California; sequence capture; RAD‐seq; transcriptomes; microfluidics; phylogenomics; genome skimming
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.1038

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.