AUTHOR=Wang Jie , Kan Junhu , Wang Jie , Yan Xinlin , Li Yi , Soe Thida , Tembrock Luke R. , Xing Guoming , Li Sen , Wu Zhiqiang , Jia Minlong 

TITLE=The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1404071

DOI=10.3389/fpls.2024.1404071

ISSN=1664-462X

ABSTRACT=<sec><title>Backgrounds</title><p><italic>Prunus mume</italic> in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated.</p></sec><sec><title>Methods</title><p>We <italic>de novo</italic> assembled a total of 322 complete <italic>P. mume</italic> plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of <italic>P. mume</italic>. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of <italic>Prunus</italic> genus, and resolved the population structure of <italic>P. mume</italic>. We also examined the nucleotide variation of <italic>P. mume</italic> to find potential DNA barcodes.</p></sec><sec><title>Results</title><p>The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of <italic>Prunus</italic> to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved.</p></sec><sec><title>Conclusion</title><p>This study constructed the pan-plastome of <italic>P. mume</italic>, which indicated the domestication of <italic>P. mume</italic> involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in <italic>Prunus</italic> and the population structure of <italic>P. mume</italic> provide an important maternal history for <italic>Prunus</italic> and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.</p></sec>