The Complete Mitochondrial Genome of the Donganyellow Chicken and Its Phylogenetic Analyses

ABSTRACT

Donganyellow chicken (Gallus gallusdomesticus, DYC) is one of the famous native breeds of Hunan province in China. It is the first time that the complete mitochondrialgenome sequence of DYC was reported. The total length of the mtDNA is16, 786bp. It contains 22transfer RNA genes, 2 ribosomal RNA genes,13 protein-coding genes and 1 D-loop region. The overall composition of the mtDNA is 30.27% for A, 23.74% for T, 32.50% for C and 13.49% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed20Galliformes species are divided into three major clades: Phasianidae, Numidiidae and Odontophoridae. In addition, our work confirmed that DYCand Taoyuan chickenhave a closegenetic relationship with fellow tribal members Xuefeng black-boned chicken and Huang Lang chicken. This work will provide an important data set for the study in genetic mechanism of chicken in Hunan province.

Keywords:
Gallus gallusdomesticus; Donganyellow chicken; mitochondrial; phylogenetic analyses

INTRODUCTION

Donganyellow chicken (Gallus gallusdomesticus, DYC), is one of the important indigenous protected breeds of chicken in Hunan Province, which has been bred in Dongan county for hundreds of years. The features of DYC is strong adaptability, good stress resistance and good meat quality (Chen, 2013). In addition, domestic chickens (Gallus gallusdomesticus) play the keyrole in the agricultural and economic sectors in Hunan Province. There are numerous domestic chicken breeds in Hunan Province including Taoyuan chicken (TYC), Huang Lang chicken (HLC), Xuefeng black-boned chicken (XBC) and DYC. However, a better characterization of the complete mitochondrial genome and genetic diversity of four domestic chicken breeds mentioned above is in urgent need to increase the conservational application for these four species.

MATERIALS AND METHODS

Determination and analysis of the complete mitochondrial genome sequence of DYC

This study determined complete mitochondrial DNA sequence of DYC, which has been registered in GenBank under accession number KM886937. The chicken was farmed at Hunan Dongan Chicken Technology Co., Ltd. (Yongzhou City, Hunan Province, China). Mitochondrial DNA of DYC was extracted using the EasyPure Kit of Genomic DNA (Transgen Biotech, Beijing, China) according to its instruction manual. PCR was carried out to amplify the complete mitochondrial genome with 11 pairs of primers. PCR products of the Gel electrophoresis were purified by Gel Advanced^TM Gel Extraction (Rich Biotech, Taiwan, China) and sequenced by BioSune Biotech (Shanghai, China). The mitochondrial DNA sequence was analyzed using DNAStar.Lasergene.v7.1 software, tRNA Scan-SE1.21 software and DOGMA software.

Phylogenetic analysis

Phylogenetic analysis was performed using the complete mitochondrial DNA sequences of 20Galliformes. Each of the sequence dataset was aligned by ClustalXand analyzed by neighbor-joining (N-J) in MEGA 4.0, and bootstrap analysis was performed with 100 replications.

RESULTS AND DISCUSSION

The total length of the mtDNA is 16,786bp. It contains the typical structure, including 24 RNA genes, 13 protein-coding genes and 1 D-loop region as that of most other vertebrates (Lin et al. 2016a). The overall composition of the mtDNA was estimated to be 30.27% for A, 23.74% for T, 32.50% for C and 13.49% for G. All the protein initiation codons are ATG, except for COX1 which is GTG (Table 1). All the mtDNA genes were encoded on the heavy (H) strand except for eight types of tRNA genes and ND6 gene. All these genes have15 spaces in the length of 1-9bpand have 7 overlaps in the length of 1-10 bp. These genes had four types of termination codons, including TAA, TAG, AGG and ‘‘T- -’’, ‘‘T- -’’ is the 5’ terminal of the adjacent gene (Anderson et al. 1981). The lengths of 12S rRNA and the 16S rRNA were 975bp and 1623bp.Among 13 protein-coding genes, the longest one was ND5 gene (1818 bp) and the shortest one was ATPase8 gene (165bp). And deduced 22 tRNA genes were distributed in rRNA and protein-coding genes, ranging from 66 to 76 bp in size, and the situation was similar to other breeds of chicken in Hunan province(Yu et al. 2016; Liu et al. 2016a; Liu et al. 2016b). The D-loop region was located between tRNA^Glu and tRNA^Phe with a length of 1232bp. The putative origin for light strand replication (OLR) had been identified in the tRNA^Trp-tRNA^Ala-tRNA^Asn-tRNA^Cys-tRNA^Tyr region (WANCY) of most vertebrates (Lin et al. 2016b; Wang et al. 2008). However, DYC might be associated with the deletion of OLR between tRNA^Asn and tRNA^Cys genes, which cannot be folded into a OLR-like secondary structure.

Table 1
Organization of the mitochondrial genome of Dongan yellow chicken.

Gene name	Position		Size	Codon		Anti-codon	Strand	Space/overlap+
	Start	End		Start	Stop
D-loop	1	1232	1232
tRNA Phe	1233	1302	70			GAA	H
12S rRNA	1303	2277	975				H
tRNA Val	2278	2350	73			TAC	H
16S rRNA	2351	3973	1623				H
tRNA Leu	3974	4047	74			TAA	H
ND1	4057	5031	975	ATG	TAA		H	9
tRNA Ile	5032	5103	72			GAT	H
tRNA Gln	5109	5179	71			TTG	L	5
tRNA Met	5179	5247	69			CAT	H	-1
ND2	5248	6288	1041	ATG	TAG		H
tRNA Trp	6287	6362	76			TCA	H	-2
tRNA Ala	6369	6437	69			TGC	L	6
tRNA Asn	6441	6513	73			GTT	L	3
tRNA Cys	6515	6580	66			GCA	L	1
tRNA Tyr	6580	6650	71			GTA	L	-1
COX1	6652	8202	1551	GTG	AGG		H	1
tRNA Ser	8194	8268	75			TGA	L	-9
tRNA Asp	8271	8339	69			GTC	H	2
COX2	8341	9024	684	ATG	TAA		H	1
tRNA Lys	9026	9093	68			TTT	H	1
ATPase8	9095	9259	165	ATG	TAA		H	1
ATPase6	9250	9933	684	ATG	TAA		H	-10
COX3	9933	10716	784	ATG	T- -		H	-1
tRNA Gly	10717	10785	69			TCC	H
ND3	10786	11137	352	ATG	TAA		H
tRNA Arg	11139	11206	68			TCG	H	1
ND4L	11207	11503	297	ATG	TAA		H
ND4	11497	12874	1378	ATG	T- -		H	-7
tRNA His	12875	12943	69			GTG	H
tRNA Ser	12944	13010	67			AGA	H
tRNA Leu	13011	13081	71			TAG	H
ND5	13082	14899	1818	ATG	TAA		H
Cytb	14904	16046	1143	ATG	TAA		H	4
tRNA Thr	16050	16118	69			TGT	H	3
tRNA Pro	16119	16188	70			TGG	L
ND6	16195	16716	522	ATG	TAA		L	6
tRNA Glu	16719	16786	68			TTC	L	2

• T- - means incomplete termination codon. ⁺Negative numbers indicate overlapping nucleotides.

An N-J tree showed that the analyzed species are divided into three major clades: Phasianidae, Numidiidae and Odontophoridae, moreover, the outgroup, Anseranser, is located at the base of the tree (Figure 1). Phasianidae makesup the first lineage, which is sister to the second group, Numidiidae; Odontophoridae forms the third group and is sister to Phasianidae and Numidiidae. This N-Jtree generated from the complete mitochondrial DNA for 20 Galliformes species have basically similar topologies. Three major branches are represented: Phasianidae, Acrylliumvulturinum and Colinus virginianus.The first lineage, subfamily Phasianidae, includes species of tribes Gallus, Bambusicola, Pavo, Tetraophasis, Meleagris, Phasianus, Chrysolophus and Coturnix. Acrylliumvulturinum is the sole member of the second group Numidiidae. The Phasianidae and Numidiidae are sister groups, which then group together with Colinus virginianus (Odontophoridae). Therefore, our work confirmed that DYC and TYC have a closegenetic relationship with fellow tribal members XBC and HLC (The overall average genetic distance between the complete mitochondrial genome sequences is 0.127). Meanwhile, we also found that DYC and TYC have highly similar genetic relationship which are consistent with those reported previously (Zhao et al. 2016).

Figure 1
Phylogenetic analysis based on complete mitochondrial genome sequences. An N-J tree was built based on the phylogenetic analysis of 20Galliformes species’ complete mitochondrial genomes. The mitochondrial genome sequences of the Galliformes species were obtained from the GenBank databases (Accession numbers have marked on the figure). Abbreviation of species indicates: DYC, Donganyellow chicken; TYC, Taoyuan chicken; XBC, Xuefeng black-bonedchicken; HLC, Huang Lang chicken.

ACKNOWLEDGEMENTS

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article. This research was supported by International S&T Cooperation Program of China (ISTCP, 2013DFG31810) and Science & Technology Project of Hunan Province (HHN2017SC09).

REFERENCES

• Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature 1981;290(5806):457-465.
• Chen K.W. Grand view of newly found local poultry varieties in China (III). China Poultry 2013;35:31-35.
• Lin Q, Cao R, Jiang GT, Qiu L, Hu GB, Dai QZ, et al. The complete mitochondrial genome of the Xupu goose. Mitochondrial DNA 2016a;27(2):1010-1011.
• Lin Q, Jiang GT, Cao R, Yun L, Li GJ, Dai QZ, et al. Determination and analysis of the complete mitochondrial genome sequence of Wugangtong grey goose. Mitochondrial DNA 2016b;27(2):1008-1009.
• Liu LL, Xie HB, Yang YS, Yu QF, He JH. The complete mitochondrial genome of the Xuefeng black-boned chicken. Mitochondrial DNA 2016a;27(1):30-31.
• Liu LL, Xie HB, Yu QF, He SP, He JH. Determination and analysis of the complete mitochondrial genome sequence of Taoyuan chicken. Mitochondrial DNA2016b;27(1):371-372.
• Wang CH, Chen Q, Lu GQ, Xu J, Yang Q, Li S. Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae. Gene 2008;424(1-2):96-101.
• Yu QF, Liu LL Fu CX, He SP, Li S, He JH. The complete mitochondrial genome of the Huang Lang chicken. Mitochondrial DNA 2016;27(1):216-217.
• Zhao FP, Fan HY, Li GH, Zhang BK. Complete mitochondrial genome sequence and gene organization of Chinese indigenous chickens with phylogenetic considerations. Genetics and Molecular Research 2016;15(2):gmr.15028200.

Publication Dates

• Publication in this collection
  2019

History

• Received
  23 Mar 2018
• Accepted
  27 Aug 2018