Taxonomic conflicts in Prunus were reported by Waugh (1901) and Hedrick (1911). Waugh (1901) stated that “plums grow pretty much as they please, and the botanist has to take them as he finds them.” He recognized that new classifications sometimes changed the previously published species groupings and classifications. Prunus classifications and discrepancies were well summarized by Bortiri et al. (2001), with Rehder’s (1940) classification being recognized as the most widely used and accepted. Rehder’s (1940) classification divided Prunus into five subgenera: Prunophora (Prunus), Amygdalus, Cerasus, Padus, and Laurocerasus. The subgenus Prunus was further divided into sections: Euprunus, Prunocerasus (North American plums), and Armeniaca. Recent phylogenetic studies supported the concept of Prunus as a monophyletic group (single genus). However, the genus Prunus contained several poorly supported subclades/terminals (subgenera/species) (Bortiri et al., 2001, 2002, 2006; Kaneko et al., 1986; Katayama and Uematsu, 2005; Lee and Wen, 2001; Shaw and Small, 2004, 2005; Wen et al., 2008).
The genus Prunus is globally distributed, with ≈200 species. North America is an important center of diversity for plum species adapted to divergent climates and soils. Plums are considered to harbor the greatest diversity of fruit flavor, aroma, texture, color, form, and size among the stone fruits (Hedrick, 1911; Waugh, 1901). Mason’s (1913) and Rehder’s (1940) taxonomic classifications have been used for most of the Prunus phylogenetic analyses. Hereafter, the North American plums will be referred to as section Prunocerasus (Bortiri et al., 2001; Shaw and Small, 2004).
The phylogeny of the genus Prunus was studied by Mowrey and Werner (1990) using isozymes. Prunus section Prunocerasus was found to be polyphyletic, with a clade composed of Prunus americana, Prunus munsoniana, Prunus hortulana, Prunus subcordata, and Prunus angustifolia, and with Prunus maritima and Prunus umbellata in another. Badenes and Parfitt (1995) reported similar results to Mowrey and Werner (1990) using cpDNA sequences. They recovered all conventional subgenus classifications based on Rehder’s (1940) taxonomic treatment: P. persica-Prunus dulcis, Prunus domestica-Prunus salicina, and Prunus cerasus-Prunus fruticosa monophyletic clades.
Two major groups, the Amygdalus-Prunus group and the Cerasus-Laurocerasus-Padus group, were recovered by Lee and Wen’s (2001) phylogenetic analysis using ITS sequences of ribosomal DNA. These results were not congruent with Rehder’s (1940) taxonomic treatment. Bortiri et al. (2001) supported the genus Prunus monophyly using ITS and chloroplast trnL-trnF spacer DNA sequences. Subgenera Padus-Laurocerasus-Cerasus and subgenera Prunus-Amygdalus-Emplectocladus-Cerasus (section Microcerasus)-section Penarmeniaca formed two major clades, respectively. The plums of northeastern North America were found to be closely related with Prunus mexicana as sister to the rest of this clade.
Bortiri et al. (2002) used the nuclear gene sorbitol 6-phosphate dehydrogenase (s6pdh) combined with ITS and trnL-trnF sequences to improve the lack of definition for deep nodes in the subgenera Prunus-Amygdalus-Emplectocladus clade, as previously reported (Bortiri et al., 2001). Phylogenetic analysis of the combined data supported two major clades: subgenera Cerasus-Laurocerasus-Padus and subgenera Amygdalus-Emplectocladus-Prunus. Section Microcerasus (subgenus Cerasus) was found nested within subgenus Prunus.
Prunus subgenus Prunus section Prunocerasus was reported to be monophyletic by Shaw and Small (2004) based on the data from seven cpDNA regions: rpS16, rpL16, trnL, trnG, trnL-trnF, trnS-trnG, and trnH-psbA. Three clades were strongly supported in section Prunocerasus based on Waugh’s (1901) classification: “American Clade,” “Chickasaw Clade,” and “Beach Clade.” The American Clade included P. americana var. americana, P. americana var. lanata, P. mexicana, Prunus rivularis, P. hortulana, P. umbellata var. injucunda; the Chickasaw Clade included P. angustifolia, P. munsoniana, Prunus gracilis, Prunus nigra, P. umbellata var. umbellata, Prunus alleghaniensis var. alleghanienses, and P. alleghaniensis var. davisii; and the Beach Clade included Prunus geniculata, P. maritima var. maritima, and P. maritima var. gravesii.
The majority of phylogenetic research in Prunus has been done using cpDNA sequences (Badenes and Parfitt, 1995; Bortiri et al., 2001, 2002, 2006; Kaneko et al., 1986; Katayama and Uematsu, 2005; Shaw and Small, 2004, 2005; Wen et al., 2008). The advantages and disadvantages of using cpDNA for plant phylogenetic analyses have been well summarized by Soltis and Soltis (1998). One of the advantages includes that the chloroplast genome of plants is small. The size of the peach (cv. Hakuhou) chloroplast genome has been estimated to be about 152 kb (Katayama and Uematsu, 2005). The chloroplast genome rate of evolution is considered to be slow in comparison with nuclear genes (Soltis and Soltis, 1998). The latter could be considered an advantage when studying distantly related species and disadvantage when studying closely related species and species at the population level. The maternal inheritance of chloroplasts can be used to track interspecific introgression events, but it could lead to erroneous species relationships (Soltis and Soltis, 1998).
The slow rate of evolution of several cpDNA sequences and their value to infer phylogenetic relationships in closely related species for some angiosperms, including Prunus, was revised by Small et al. (1998) and Shaw et al. (2005, 2007). The main objective of the study of Shaw et al. (2007) was to identify chloroplast regions that would provide the greatest number of characters for low-level molecular phylogenetic studies. Shaw et al. (2007) recommended selecting the top few choices with the greatest variability to be screened in a particular lineage to determine which of those are the most informative for a specific group.
Bortiri et al. (2006) demonstrated the power of including morphological characters for Prunus phylogenetic analyses. The combined data provided by ITS sequences, cpDNA regions, and morphological characters for Prunus yielded support of some nodes that were previously identified in Prunus (Bortiri et al., 2001). Several synapomorphies supported large groups, providing additional resolution for some clades. Similarly, Rohrer et al. (2004) reported that microsatellite markers could provide the genetic variability necessary to resolve the relationships within Prunus at the species level.
The main objective of this research was to measure and to identify additional genomic regions that could provide the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level for Prunus section Prunocerasus relationships.
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