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An introduction to plant phylogenomics with a focus on palms

Journal article
Authors C. F. Barrett
Christine D. Bacon
Alexandre Antonelli
A. Cano
Tobias Hofmann
Published in Botanical Journal of the Linnean Society
Volume 182
Issue 2
Pages 234-255
ISSN 0024-4074
Publication year 2016
Published at Department of Biological and Environmental Sciences
Pages 234-255
Language en
Links doi.org/10.1111/boj.12399
Keywords arecaceae, arecales, bioinformatics, genomics, high throughput sequencing, next generation, multispecies coalescent model, westslope cutthroat trout, species trees, phylogenetic inference, sequence data, gene trees, oil palm, ultraconserved elements, evolutionary analysis, population genomics, Plant Sciences
Subject categories Environmental Sciences

Abstract

Phylogenomics refers to the use of phylogenetic trees to interpret gene function and genome evolution and to the use of genome-scale data to build phylogenetic trees. The field of phylogenomics has advanced rapidly in the past decade due to the now widespread availability of next generation sequencing technologies, which themselves continue to change at a rapid pace and drive down the cost of sequencing per base pair. In this review, we discuss genomic resources available to palm biologists in the form of complete genomes (plastid, mitochondrial, nuclear) and sequenced transcriptomes, all of which can be leveraged to study non-model palm taxa. We also discuss various approaches to generating phylogenomic data in palms, such as next-generation sequencing technologies and methodological approaches that allow acquisition of large volumes of biologically and phylogenetically meaningful data without the need to sequence entire genomes (e.g. genome skimming, RAD-seq, targeted sequence capture). This review was designed for those unfamiliar with phylogenomics and associated methods, but who are interested in engaging in phylogenomics research. We discuss several considerations required for designing phylogenetic projects using genomic data, such as available computing capabilities and level of bioinformatics expertise. We then review some recent, empirical examples of palm phylogenomic studies and how they are shaping the future of palm systematics and evolutionary biology.

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