The Bioinformatics Analysis in the Whole Genome mtDNA Sequence of Chickens ( Gallus gallus )

Abstract

Chicken is important livestock in the world that is kept for egg and meat productions. This study was aimed to perform a bioinformatics analysis in the whole genome mtDNA (16,979 bp) of many chicken breeds. Total 84 whole-genome mtDNA sequences were used in this study and obtained from the reference sequence (GenBank). Four molecular packages of BioEdit, MEGA-X, DNAsp, and Arlequin were used in this study to analyze the observed sequences. Therefore, the whole genome mtDNA sequence of birds in this study was originated from Asia, the USA, and New Guinea. Research showed that a total of 445 mutation sites and 81 haplotypes were obtained in this study. Thus, the nucleotide diversity in the observed sequences included of high (0.99). In addition, a total of 10 clusters were observed according to the phylogenetic analysis with the UPGMA method. In conclusion, a close genetic relationship was observed among chickens of Asia based on the median-joining network. Meanwhile, the geographical factors were contributed about 9.12% in a sequence variation.