Plastome analysis of cultivated apricots: genome structure, nucleotide diversity, and phylogeny

The genetic diversity and evolution of plastomes in P. armeniaca L. (common/cultivated apricot) have been poorly studied.Complete plastomes of 20 accessions and 10 F1 hybrids, identified as P. armeniaca L., were de novo assembled filtering from total DNAnt reads. These plastomes were subsequently analyzed with the Prunus genus accessions retrieved from the GenBank. The plastomesexhibited conservation of genomic structure, gene organization and order, with lengths ranging from 158,057 nt to 158,089 nt,displaying a narrow size variation. Except for “Zard” and its hybrids, the plastomes of apricot genotypes from different regions showedonly three haplotypes, indicating narrow genetic diversity in cultivated P. armeniaca accessions. “Zard” and its hybrids exhibited thehighest identity with P. mandshurica Maxim (Manchurian apricot), demonstrating the significance of plastome analysis for the accurateidentification of apricots. Further, while the three apricot species, P. armeniaca, P. mandshurica, and P. mume Sieb. (Japanese apricot),were grouped as sister clades, P. sibirica L. (Siberian apricot) exhibited the highest nucleotide identity with P. cerasifera Ehrh. (Cherryplum), contrary to conventional morphological systematics of apricots. Additionally, the plastomes of hybrids obtained in this studysupported maternal inheritance of the plastome. These results reveal the evolutionary relationship among apricots and will serve as aframework for future comparative studies on Prunus evolution.