The Phylogeny of the North American Plums (Prunus spp.)

The genus Prunus L. constitutes approximately 200 species distributed worldwide. Plums, cherries, almonds, apricots, and peaches belong to this genus. North America is a center of diversity for the genus Prunus. The phylogeny of the North American plums has been previously studied using chloroplast DNA (cpDNA) and internal transcribed spacer regions (ITS) sequences. However, phylogenetic studies based solely on cpDNA information could be biased due to hybridization among Prunus species. The objective of this research was to use nuclear markers and cpDNA to recognize possible incongruence events and to improve the knowledge of the phylogenetic relationships of these species. The University of Florida Stone Fruit Breeding and Genetics Program in collaboration with the National Germplasm Repository and USDA-ARS (Project No. 5306-21000-018-00D) collected and identified 408 accessions of 35 taxa from the wild. Approximately 62 amplicons representing cpDNA, and enzyme, branching and dormancy related genes, were sequenced and studied for a core collection of 13 species representing section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, and LFY amplicons, were identified as having the highest frequency of potentially informative characters and the phylogenetic signal across samples within subgenus Prunus section Prunocerasus. A total of 105 accessions (out of the 408) representing 35 taxa, with approximately 2-3 accessions per species, were used to study the phylogeny of the North American plums using trnH-psbA, PGI, MAX4, AXR1, and LFY amplicons. Subgenus Prunus section Prunocerasus was represented by 14 taxa, commonly accepted as North American plums. Other groups within genus Prunus were represented by an additional 21 species: sect. Armeniaca (2), sect. Penarmeniaca (3), sect. Prunus (1), sect. Microcerasus (1) in subgenus Prunus; subgenus Emplectocladus (1); sect. Cerasus (5) and sect. Laurocerasus (3) in subgenus Cerasus; and subgenus Amygdalus (5) (USDA-ARS and GRIN taxonomic classifications). The use of nuclear markers improved the support for some species relationships and identified novel species relationships. Several sources of incongruence between cpDNA and nuclear genes were identified. Three major clades within section Prunocerasus were identified: the Sand clade, the American clade, and the Chickasaw clade. The Sand clade was constituted by P. texana and P. geniculata. The American clade was composed by P. americana, P. alleghaniensis, P. mexicana, P. hortulana, and P. rivularis. The Chickasaw clade was formed by P. angustifolia, P. gracilis, P. maritima, P. munsoniana, P. nigra, and P. umbellata.