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About the Authors:
Allison J. Miller
* E-mail: [email protected] (AM); [email protected] (SM)
Affiliation: Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
Naim Matasci
Affiliation: Department of Ecology and Evolutionary Biology and iPlant Collaborative, University of Arizona, Tucson, Arizona, United States of America
Heidi Schwaninger
Affiliation: United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
Mallikarjuna K. Aradhya
Affiliation: United States Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, University of California Davis, Davis, California, United States of America
Bernard Prins
Affiliation: United States Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, University of California Davis, Davis, California, United States of America
Gan-Yuan Zhong
Affiliations United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America, United States Department of Agriculture, Agricultural Research Service, Grape Genetic Research Unit, New York Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
Charles Simon
Affiliation: United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
Edward S. Buckler
Affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
Sean Myles
* E-mail: [email protected] (AM); [email protected] (SM)
Affiliation: Faculty of Agriculture, Dalhousie University, Truro, Canada
Introduction
Understanding relationships among species is the basis for modern classification schemes and provides the requisite framework for ecological and evolutionary analyses of diversity patterns and diversification processes [1], [2]. Large-scale coordinated research programs, together with technical and analytical advances, have facilitated significant progress in current understanding of organismal phylogeny. Despite this, uncertainty regarding evolutionary relationships among species remains in many groups, including several that include economically important species such as apples [3], [4], grapes [5]–[7], potatoes [8], and wheat [9].
Over the past five years, nearly all sub-disciplines within biology have been revolutionized in the wake of the genomics era [10], [11]. Widespread adoption of next-generation sequencing (NGS) technologies have reduced the cost of DNA sequencing by orders of magnitude providing unprecedented access to the genome of...