Comparative and phylogenetic analyses of the chloroplast genome reveal the taxonomy of the genus.

Mulberry (genus ) is an economically important woody plant with an altered ploidy level. The variable number of species recognized by different studies indicates that the genus is in need of revision. In this study, the chloroplast (CP) genomes of 123 varieties were assembled and systematically analyzed. The 123 varieties represented six species, namely, , , , , , and . The CP genome was found to be 158,969~159,548 bp in size with 125 genes, including 81 protein coding, 36 tRNA, and 8 rRNA genes. The 87 out of 123 mulberry accessions were assigned to 14 diverse groups with identical CP genome, which indicated that they are maternally inherited and share 14 common ancestors. Then 50 diverse CP genomes occurred in 123 mulberry accessions for further study. The CP genomes of the genus with a quadripartite structure have two inverted repeat (IR) regions (25,654~25,702 bp) dividing the circular genome into a large single-copy (LSC) region (87,873~88,243 bp) and small single-copy (SSC) region (19,740~19,994 bp). Analysis of the phylogenetic tree constructed using the complete CP genome sequences of revealed a monophyletic genus and that consisted of two clades, var. and var. . The Japanese cultivated germplasms were derived from var. . We propose that the genus be classified into six species, , , , , , and with two subspecies, var. and var. . Our findings provide a valuable resource for the classification, domestication, and breeding improvement of mulberry.