Perspectives in plant evolutionary genetics: A field guide in 15 “easy steps” to modern tools in evolutionary genetics and genomics

Plant genomes contain huge troves of information, and nowadays molecular tools to analyze genomes are less expensive and keep improving. In this review, we aimed to produce a “roadmap” to take advantage of this explosion of molecular methods and opportunities. We explain how to decide which strategies are adequate for a given evolutionary or taxonomic problem by describing 15 possible (and in some cases nonconsecutive) steps to take advantage of all the genomic resources drawing from the ever-increasing studies. We describe how to obtain an adequate genome sequence given our study species and objectives and discuss if we need to also obtain a transcriptome and additional “omic” data ( i.e. , proteome, metabolome, epigenome, microbiome). We analyze what is needed to conduct population genomics studies in terms of genomic methods and sampling strategies and discuss the pangenome concept. In addition, we present some considerations about how to estimate population genetics parameters and how to analyze geographic differentiation, inbreeding and gene flow. We examine ideas and methods on how to estimate natural selection and local adaptation, how to detect candidate genes, how coalescent analyses can help in these studies, the importance of genomic information for conservation studies and to understand adaptability to climate change. We assess the use of these methods in domestication studies and in understanding how form and function can be inferred from genes; likewise, how to use the genomic information for improvement of cultivated plants. We also review how can we use these methods in phylogenomic studies.