D-Loop DNA genome sequence of Donggala cattle by using Nanopore analysis

Abstract

Donggala cattle have been breed for generations, making them a valuable genetic resource for Indonesian livestock species in Central Sulawesi that must be protected and preserved. Donggala cattle which certainly has potential as a regional germplasm resource and study focuses on the analysis in the mitochondrial DNA D-Loop region from liver tissue. This study aimed to determine the complete mtDNA sequencing was performed using WGS mtDNA analysis with nanopore technology by Oxford Nanopore Technologies GridION. Bioinformatics and data analysis were then performed. Results: This study showed that the length of the mtDNA genome is 16,412 bp, consisting of two ribosomal comprises 27 genes with a typical structure. These include 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and noncoding D-loop region, a total of 505 site variations in the D-Loop region The variable site (49%), parsimony (57%) and singleton (43%). Phylogenetic analysis based on the complete mitochondrial genome sequences distinguished into three clades of cattle breed. Including B. javanicus (GenBank data PQ 130485 and PV387265), B. gaurus, B. grunienns and Bali indicus cattle groups showed notable genetic variations. The results of this work offer genomic information capable of supporting the next investigations on the genetic structure and evolutionary background of Donggala cattle.