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. 2022 Nov 4;12(21):3037.
doi: 10.3390/ani12213037.

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

Sihua Jin  1   2 , Jingjing Xia  1   2 , Fumin Jia  1   2 , Lijun Jiang  1   2 , Xin Wang  1   2 , Xuling Liu  1   2 , Xing Liu  1   2 , Zhaoyu Geng  1   2
Affiliations

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

Sihua Jin et al. Animals (Basel). .

Abstract

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.

Keywords: D-loop region; Pingpu Yellow chicken; mtDNA; phylogeny.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The geographical location of the Pingpu Yellow chicken.
Figure 2
Figure 2
Mitochondrial genome structure of the Pingpu Yellow chicken. Genes in the inner circle plot are located on the N-strand, and the rest of the genes are located on the J-strand. Dark green, light green, and yellow represent PCGs coding complex I, III, and IV, respectively. ATP synthase, rRNA, tRNA genes, and the control region are colored with olive green, red, dark blue, and gray, respectively.
Figure 3
Figure 3
Relative synonymous codon usage (RSCU) in the Pingpu Yellow chicken mitochondrial genome.
Figure 4
Figure 4
The inferred secondary structure of 22 tRNA genes from the Pingpu Yellow chicken.
Figure 5
Figure 5
Median-joining network of chicken mtDNA D-loop haplotypes.
Figure 6
Figure 6
Evolutionary relationships of the Pingpu Yellow chicken and other chicken breeds.
See this image and copyright information in PMC

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