Molecular Markers for Mulberries: Chloroplast Phylogenomics Support Monophyly of the Genus Morus — 4a — Bibek Adhikari, Sanam Parajuli and Madhav P. Nepal

The Genus Morus (Family: Moraceae) comprises 13 species distributed across the world except in Antarctica. The North American Native Red Mulberry (Morus rubra) is primarily found within the heart of pristine forests of riparian areas. Introgressive hybridization of M. rubra with the invasive introduced congener White Mulberry (M. alba) has severely threatened the species integrity of M. rubra. We sampled 45 mulberry trees representing populations from eight different US states for chloroplast genome sequencing. We analyzed both chloroplast and nuclear DNA markers for their applications in DNA fingerprinting at the population level, as well as in phylogenetic inference of all species within the genus. The chloroplast genome of M. rubra ranged from 159,396-159,423 bp and included 128 genes coding for eight rRNAs, 37 tRNAs, and 83 proteins. The chloroplast genome size of M. rubra was 104 bp larger than that of M. alba. The DNA sequence polymorphism analysis of the chloroplast genomes showed the presence of 13 haplotypes – 12 belonging to M. rubra and a single M. alba type. As expected, the non-coding and intergenic spacer regions were more variable than the coding sequences. The phylogenomic analysis of 12 Morus species based on cp genome revealed the distinct clades for Asian, North American, South American, and African Morus supporting the monophyly of the genus Morus. Nine hypervariable sites were observed with the possibility of species-specific markers which are yet to be tested. The results from this study provide insight into the chloroplast genome structure of M. rubra and provide foundational data for addressing complex taxonomic issues within the genus, and molecular markers for understanding population genetics including introgressive hybridization.

KEYWORDS: Endangered Species, Chloroplast Genome Sequencing, Introgressive Hybridization, Molecular Markers, Morusrubra, Morus Phylogeny, Native-Invasive Hybridization, Red Mulberry, Phylogenomics of Mulberries

South Dakota State University
Madhav P. Nepal