Complete Mitochondrial Genome, Genetic Diversity and Phylogenetic Analysis of Pingpu Yellow Chicken (Gallus gallus)

Simple Summary Characterization of the complete mitochondrial genome can provide information regarding important genomic features, such as genome size and the relative location of genes, and is widely used in studies on genetic diversity and phylogeny of animals. The displacement loop region (D-loop) of mitochondrial DNA (mtDNA) is considered to be a beneficial molecular marker for genetic distance determination and differentiation analysis. This study presents the mtDNA diversity and genetic characterization of Pingpu Yellow chicken (PYC) breeds, including insights into their genetic background. The median-joining (MJ) network showed that the haplotypes were clustered into all three haplogroups (A, B, and C), indicating that PYC may have three maternal origins. The phylogenetic tree constructed with the neighbor joining (NJ) method based on the full mitogenomes showed that the 21 chicken breeds could be separated into two groups. In this study, the complete mitochondrial genome sequence of one female Pingpu Yellow chicken (PYC) and the D-loop sequences obtained from 60 chickens were analyzed to investigate their genetic diversity and phylogeny. The total length of the PYC mitogenome is 16,785 bp and that of the complete D-loop is 1231 to 1232 bp. The mitogenome comprises 22 transfer ribonucleic acids (tRNAs), 2 ribosomal ribonucleic acids (rRNAs), 13 protein-coding genes (PCGs), and 1 non-coding control region (D-loop). Additionally, the total length of the 13 PCGs is 11,394 bp, accounting for 67.88% of the complete mitogenome sequence, and the PCGs region has 3798 codons. A majority of the PCGs have ATG as the start codon. The haplotype and nucleotide diversity of PYC were 1.00000 +/- 0.00029 and 0.32678 +/- 0.29756, respectively. In the D-Loop data set, we found 25 polymorphic sites, which determined 18 haplotypes and 3 major haplogroups (A-C). Therefore, PYC has a classical vertebrate mitogenome, with comparatively high nucleotide diversity and potentially three maternal lineages. The neighbor-joining (NJ) tree analysis results showed PYC grouped with the Luhua (MT555049.1) and Nandan chickens (KP269069.1), which indicates that PYC is closely related to these two breeds.