Phylogenomic Analyses and <scp>DNA</scp> Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution

Moraceae, with its seven tribes, 45 genera, and approximately 1200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogeny of Moraceae species remains challenging due to their diverse morphological features. To address this issue, we sequenced seven complete plastomes and analyzed online datasets for 46 other species at the tribal level within Moraceae. Our analysis revealed that all the plastomes within this family had a typical quadripartite structure and ranged from 158,459 to 162,594 bp in length. Comparative plastome analyses revealed 10 highly variable regions (<i>ndhF</i>-<i>rpl32</i>, <i>rps4</i>-<i>trnT</i>, <i>rps15</i>-<i>ycf1</i>, <i>trnC</i>-<i>petN</i>, <i>ycf1</i>). A total of 5350 dispersed and tandem repeats along with 4751 simple sequence repeats (SSRs) were identified, highlighting their potential for the development of molecular markers in Moraceae. While the evolutionary rates across the various tribes of Moraceae were found to be similar, the genes <i>ndhK</i>, <i>ndhD</i>, <i>rps2</i>, and <i>rps12</i> displayed evidence of positive selection. Codon usage bias was shaped by mutation and selection, with significant natural selection observed on genes such as <i>clpP</i>, <i>ndhC</i>, <i>ndhI</i>, etc. Additionally, 13 optimal codons were identified for 10 genes. This study confirms that the seven tribes within the Moraceae family are monophyletic, with divergence estimated to have occurred approximately 79.43 million years ago. This timing coincides with the formation of modern rainforests and a burst in angiosperm diversity toward the end of the Cretaceous period. Overall, the resolution of Moraceae tribal-level phylogeny provides a foundational framework for revising taxonomic classifications. Furthermore, our genomic resources will be available for genetic engineering and germplasm exploration within this versatile plant family.