Phenome, repeatome, and transcriptome analysis to comprehend the structural and functional aspects of polyploid Morus serrata Roxb

Repeat elements contribute significantly to genome expansions, gene regulation, and expression of functional traits at the increased cost of genome maintenance, especially in polyploids. Morus serrata Roxb. (Moraceae) is a wild tree species having polyploid genome of Himalayan origin. Upon phenotypic analysis, M. serrata exhibited distinct polyploid-associated traits within the Morus species complex, which are impacted by cell size, cell division rate, and stoichiometry balance. Genomic analysis suggests that genome-wide repeated DNA landscape (repeatome), especially DNA transposons played a substantial role in the genome expansions of M. serrata. Furthermore, M. serrata transcriptome yielded overrepresented genes associated with the transposition of transposable elements (TEs) and nucleic acid metabolism. Overall phenome, repeatome, and transcriptome study reveals that M. serrata devotes a significant portion of its transcriptional budget to maintaining a large genome expended by TEs and loses growth superiority compared to studied species of the genus Morus L. The study provided new insights into the structural and functional aspects of natural polyploidization and loss of growth superiority.