Supplemental File 1
Multiple sequence alignment showing the single nucleotide polymorphisms (SNPs) and insertions-deletions (indels) in the spacer between (A) rps4-trnT-UUG, (B) psbC-trnS-UAG, (C) psbZ-trnG-GCC, (D) trnG-GCC-trnM-CAU, (E) trnS-GCU-trnG-UCC, (F) psbF-petL, and (G) trnL-UAA-trnF-GAA genes of 45 sequenced specimens with the potential of developing molecular markers in separating Morus rubra and Morus alba chlorotypes. First 10 sequences from PQ309062-PQ309071 represent M. alba and the remaining PQ309062 - PQ309106 represent M. rubra.

SF1: Phylogenetic tree based on the concatenated rps4-trnT-UUG, psbC-trnS-UAG, psbZ-trnG-GCC, trnG-GCC-trnM-CAU, trnS-GCU-trnG-UCC, psbF-petL, and trnL-UAA-trnF-GAA sequences showing distinct clades for M. alba and M. rubra. Artocarpus heterophyllus was used as an outgroup. Legend denotes the grouping of the samples (represented by the NCBI Accessions).
