title: Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function.
abstract: Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.
authors.affiliation: Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada.
authors.forename: Julien
authors.initials: J
authors.lastname: Prunier
authors.affiliation: Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany.
authors.forename: Jukka-Pekka
authors.initials: JP
authors.lastname: Verta
authors.affiliation: Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada.
authors.forename: John J
authors.initials: JJ
authors.lastname: MacKay
mesh_terms: D000222:Adaptation, Physiological; D005075:Biological Evolution; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D064028:Tracheophyta / Q000235:genetics*
keywords: Coniferales; RNA-sequencing; gene expression; genome evolution; genomics of adaptation; next generation sequencing (NGS); speciation-by-adaptation