Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes

• Published in: Molecular phylogenetics and evolution Vol. 197; p. 108093
• Main Authors: Wang, Meizhen, Zhu, Mengmeng, Qian, Jiayi, Yang, Zhaoping, Shang, Fude, Egan, Ashley N., Li, Pan, Liu, Luxian
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-08-2024
• Subjects: Angiosperm-mega 353; Cell Nucleus - genetics; Evolution, Molecular; Genes, Plant; Genome, Plant; Hybridization; Incomplete lineage sorting; Morus - classification; Morus - genetics; Mulberry; Phylogenomics; Phylogeny; Plastome; Sequence Analysis, DNA; Mulberry; Plastome; Angiosperm-mega 353; Hybridization; Incomplete lineage sorting; Phylogenomics
• ISSN: 1055-7903; 1095-9513; 1095-9513
• DOI: 10.1016/j.ympev.2024.108093

[Display omitted]
•Mulberries (Morus) are one of the most economically and ecologically important plant groups.•The systematics of Morus is challenging due to its widespread distribution and hybridization.•The phylogeny of Morus especially for the Asian species is fully resolved using single copy nuclear genes.•There are strong phylogenetic relationships discordance of Morus.•The discordances could be explained by both hybridization/introgression and ILS.
Mulberries (genus Morus), belonging to the order Rosales, family Moraceae, are important woody plants due to their economic values in sericulture, as well as for nutritional benefits and medicinal values. However, the taxonomy and phylogeny of Morus, especially for the Asian species, remains challenging due to its wide geographical distribution, morphological plasticity, and interspecific hybridization. To better understand the evolutionary history of Morus, we combined plastomes and a large-scale nuclear gene analyses to investigate their phylogenetic relationships. We assembled the plastomes and screened 211 single-copy nuclear genes from 13 Morus species and related taxa. The plastomes of Morus species were relatively conserved in terms of genome size, gene content, synteny, IR boundary and codon usage. Using nuclear data, our results elucidated identical topologies based on coalescent and concatenation methods. The genus Morus was supported as monophyletic, with M. notabilis as the first diverging lineage and the two North American Morus species, M. microphylla and M. rubra, as sister to the other Asian species. In the Asian Morus species, interspecific relationships were completely resolved. However, cyto-nuclear discordances and gene tree-species tree conflicts were detected in the phylogenies of Morus, with multiple evidences supporting hybridization/introgression as the main cause of discordances between nuclear and plastid phylogenies, while gene tree-species tree conflicts were mainly caused by ILS.