Transcriptomic insights into developmental arrest in fluorescent labeling transgenic Asian elephant (Elephas maximus) embryos via inter-order cloning

Approximately 25% of clean reads successfully aligned with the Asian elephant genome. The transcriptomic analysis revealed that inter-order cloned embryos with earlier cleavage at the 2- and 4-cell stages exhibited signs of residual transcriptomic memory and incomplete epigenetic reprogramming, while arrested embryos showed indications of nucleocytoplasmic incompatibility and nDNA-mtDNA mismatch. Hub gene analyses indicated core genes such as <i>NDUFC2</i>, <i>NDUFS3</i>, <i>NDUFAB1</i>, <i>SDHC</i>, <i>SDHB</i>, <i>NUP54</i>, <i>NUP43</i>, <i>NUP37</i>, <i>NDC1</i>, <i>CDK1</i>, and <i>CCNB1</i> linked to energy production, nucleocytoplasmic transport, and cell cycle regulation highlighting the overall challenges in cloning Asian elephant inter-order embryos. Altogether, the analysis of high-throughput sequencing enhances the reliability of iSCNT production in this study, advancing our understanding of cellular reprogramming and molecular roadblocks in AE-P inter-order cloned embryos. Transcriptomic analyses have identified key factors contributing to developmental barriers in iSCNT, offering valuable insights into the complexities of these challenges.