Complete Mitochondrial Genome Characterization and Phylogenetics of Ongole Grade (PO) Cattle

Abstract

The Peranakan Ongole (PO) cattle are a native Indonesian breed and a vital component of the country’s livestock genetic heritage. The scarcity of mitochondrial genome data for this breed underscores the need for further research to inform future breeding programs. This study examined the mitochondrial genome of Ongole grade (PO) cattle and constructed a phylogenetic tree using both complete and partial sequences. The DNA extraction and PCR processes were conducted at the BRIN Genomics Building in Cibinong, Bogor, West Java. In addition, sequencing of the PCR products was performed at PT Genomik Solidaritas Indonesia (GSI) in South Jakarta. We analyzed blood samples from five PO bulls at the Singosari Cattle Breeding Center (BBIB), Malang, East Java, Indonesia. DNA was extracted using the Quick-DNA HMW Magbead Kit (Zymo Research, USA), and two primer pairs yielded fragments of 9,064 and 9,222 bp based on the Bos javanicus CERZA reference. Sequencing was performed using Oxford Nanopore technology. The phylogenetic analysis included full-length and specific mitochondrial regions: D-loop, Cyt-b, COX1, ND5, and 16S rRNA. The complete mitochondrial genome was 16,562 base pairs long and encoded 13 protein-coding genes, 22 tRNA genes, and the D-Loop control region. Phylogenetic trees constructed from both full and partial genomes showed consistent relationships, indicating that PO cattle are closely related to Bos javanicus CERZA (JN632606.1) and bali cattle (PQ130485.1). The study suggested that partial mitochondrial DNA markers could produce phylogenetic trees comparable to those from complete genomes. However, bootstrap support was lower with partial data, highlighting the greater resolution provided by full mitochondrial sequences.