Unravelling High Nuclear Genomic Similarity and Mitochondria Linked Epigenetic Divergence in SCNT Derived Buffalo Clones via Long-Read Nanopore Genome Sequencing.

Somatic cell nuclear transfer (SCNT) holds promise for animal cloning but remains limited by low efficiency and phenotypic abnormalities, often attributed to incomplete nuclear reprogramming. This study presents an integrative genomic and epigenomic analysis of cloned buffaloes and their respective donors using long-read Oxford Nanopore sequencing. Our results showed a high degree of genomic similarity between clones and donors, with most variations located in non-coding regions and structural variants (SV) distributions highly correlated at the chromosomal level. Gene and protein level overlap of SV-affected loci revealed 70.9-73.3% gene-level and 69.7-72.5% protein-level similarity. Despite this genetic similarity, DNA methylation analysis identified differentially methylated regions (DMRs), particularly in intergenic and promoter regions. Clones exhibited slightly lower CpG methylation than the donors. The DMRs in donor vs. clone comparisons indicated higher hypomethylated regions than hypermethylated regions. Functional enrichment of DMR-associated genes highlighted pathways linked to mitochondrial function, oxidative phosphorylation, and reproductive processes. Although clones showed moderate genome-wide methylation correlation with donors, key differences in methylation suggest incomplete epigenetic reprogramming. Despite these epigenetic differences, all clones were phenotypically normal and healthy into adulthood. This study offers the first comprehensive SV and methylome profile of SCNT-derived buffaloes and emphasizes the role of epigenetic mechanisms in clone development and health, providing valuable insights to enhance cloning efficiency.