Phylogenetic relationship in the plants of subgenus Prunophora (Rosaceae) inferred from the chloroplast DNA region, trnL-F

Abstract:【Objective】The phylogenetic classification of the economically important genus Prunus L. iscontroversial and the taxonomy of plum and apricots has changed with time, due to the high levels of convergent or the parallel evolution of morphological traits. Most pomologists considered that Prunus shouldinclude plums along with peach, cherry, apricot and almond. Integrated Taxonomic Information System(ITIS) divided the Prunophora subgenus into three sections: Euprunus section, Armeniaca section andPrunocerasus section. This study aimed to assess the phylogenetic relationships of new species in the sub⁃genus Prunophora (Rosaceae) and elucidate the possible origin and its botanical classification.【Methods】Chloroplast DNA fragments (trnL- F) of 45 accessions representing 17 species (including apricots andplums) were amplified by polymerase chain reaction (PCR) method and sequenced in this investigation.Moreover, the additional 22 sequences in the subgenus Prunophora were downloaded from GenBank, and1 accession of P. tomentosa from GenBank (AM282663) was chosen as out-group. The alignment of DNAsequences was initially performed with DNAMAN and ClustalX, then with subsequent manual adjustmentby eye. Variable positions in the data matrices were double checked against the original chromatogramfiles to make sure that all base calls were true at all variable positions. The SNPs and phylogenetic treewere analyzed using the neighbor-joining method in MEGA 6.0 software.【Results】Sequencing of trnL-Fregion was successful in all of the species. Aligned nucleotides ranged from 945 to 956 bp, and the align⁃ment matrix was 962 bp. The aligned matrix consisted of 941 invariable sites, 9 variable sites that wereparsimony un-informative and 12 parsimony-informative sites. In addition, a total of 3 phylogeneticallyinformative indels were coded for inclusion in the analysis. Based on the trnL-F spacer sequences, significant molecular characteristics were found in some species, which could be used for species identification.For instance, two specific sites of deletion fragments (AAACG) in 554 bp and mutation (T«C) in 165 bponly existed in Armeniaca section, such as P. armeniaca, P. holosericea, P. sibirica and P. mandshurica;the mutation site (A«G) in 660 bp were only detected in P. cerasifera and P. dasycarpa; the mutation site(G«A) in 288 bp occurred only in P. brigantina, P. spinosa and wild population of P. domestica; the sitespecificmutation, a single-base repeat sequences (T12), of P. ussuriensis was located in 798 bp; the specific site (A«G) of P. brigantina was only located in 931 bp. Compared with P. salicina, P. mume, P. limeixing, P. zhenghensis and P. simonii were not any of specific variation sites. We identified 20 haplotypes,which were tentatively divided into six clades. The results of phylogenetic tree showed that taxa of the subgenus Prunophora formed a well-supported clade, and within these remaining species the data were distinguished into six major clades: 1) the apricot group, including the majority of members of the Armeniacasections, P. armeniaca, P. holosericea, P. sibirica, P. mandshurica; 2) the Chinese plum group I, compris⁃ing of the majority of the P. salicina and P. simonii, and P. mume (as Armeniaca section), P. limeixing, P.zhenghensis; 3) the Chinese plum group II, including one accession of the P. salicina and all of P. ussuriensis; 4) the Asian/Eur plum group, including all the European species, and which were divided into the twogroups distributed in the wild populations (P. spinosa, P. brigantina, and wild population of P. domestica)and cultivation populations (P. cerasifera, P. dasycarpa, P. insititia and cultivation population of P. domes⁃tica); 5) only one accession of P. salicina (Fuzhou Qingnai); 6) two accessions of P. sibirica (Dashanxingand B1-10-2-1).【Conclusion】As a consequence, single trnL-F sequence could not solely used for distinguishing species in the subgenus Prunophora, and the sequences were similar in closely related species. The results were in accord with the points that P. brigantina belonged to the Euprunus section; P. limeixing and P. dasycarpa were derived from a natural interspecific hybrid with P. salicina or P. cerasiferaas its maternal progenitor and P. armeniaca as the female parent; the Euprunus section was divided intotwo non-sister sections, and all polyploidy species were closely related to the diploid species of P. cerasifera, while the P. salicina species was scattered; wild populations of domestica, P. spinosa and P. brigantina were close relatives, while cultivation populations of domestica and P. insititia were close relatives.