Study of Kosta goat (Capra hircus) mitochondrial DNA and their phylogenetic based on whole genome sequensing

Kosta goat is one of the Indonesian local goats which had the potential to utilize, while their genetics was not yet characterized. Since, a high mutation of Mitochondria DNA (mtDNA), it is widely applied to understand species evolutionary, phylogenetic, and characterized population genetics. Whole genome sequencing of Mitochondria DNA has new insight to elucidate genetic characteristic of goat completely. Therefore, this study purposes to explore the whole mitochondrial DNA of the Kosta goat and its relationship with other breeds based on Whole Genome Sequensing (WGS). The Kosta goat mitochondria genome was collected from whole blood, which was enriched using REPLI-g Mitochondrial DNA Kit (Qiagen). Oxford Nanopore Technology was employed in the mtDNA sequencing. The assembled sequence was polished with Racon and Medaka, and was further determined using Quast. Furthermore, Annotation and Visualization were conducted using MitoZ and Mitos Webserver. The sequence mitochondria genome of the Kosta goat has 16,641 bp, consisting of 13 PCGs (Protein Coding Genes), 22 tRNA, 2 rRNA, D_loop region, as well as OL (origin loop) sequences. Also, it has a base composition of 33.57 % for Adenin (A), 27.31 % for Timin (T), 26.04 % for Cytosin (C), and 13.08 % for Guanin (G), with sequential percentages of A>T>C>G. The start codons of PGCs are primarily initiated by ATG, whereas for ND2, ND3, and ND5 by ATA. Specific genetic characteristic of mitogenome Kosta goat has 309 bp length of ND3. Kosta goat belongs to Lineage B, and this follows the study of other Indonesian goats. Complete mitochondrial DNA of Kosta goats can be used to characterize their genetic potential, genetic diversity, phylogenetic analysis to support their utilization and conservation.