Complete mitochondrial genome of dong tao chicken breed (gallus gallus domesticus) of Viet Nam

Journal of Biotechnology 16(4): 589-593, 2018 589 BRIEF REPORT COMPLETE MITOCHONDRIAL GENOME OF DONG TAO CHICKEN BREED (GALLUS GALLUS DOMESTICUS) OF VIETNAM Nguyen Dang Ton*, Nguyen Hai Ha, Vu Phuong Nhung, Nguyen Thi Thanh Hoa, Ma Thi Huyen Thuong, Tran Thi Bich Ngoc, Nguyen Thuy Duong, Nong Van Hai Institute of Genome Research, Vietnam Academy of Science and Technology * To whom correspondence should be addressed. E-mail: dtnguyen@igr.ac.vn Received: 11.9.2018 Accepted: 25.12.2018 SUMMARY The complete mitochondrial genome of Dong Tao chicken breed (Gallus gallus domesticus, Dong Tao) was obtained by PCR and sequencing. The complete mitogenome was 16,783 bp in length, with the nucleotide composition for A, T, C, G was 30.29%, 23.75%, 32.48%, and 13.48%, respectively. The mitogenome of Dong Tao chicken contained a non-coding control region (D-loop), 2 rRNA genes, 13 protein-coding genes, and 22 tRNA genes. Phylogenetic analysis revealed that breed Dong Tao chicken breed was sister-close to G. gallus breed Guangxi, and paraphyletic to G. spadiceus, S. jabouillei, and a range of Chinese indigenous, ie. breeds Rugao and Taoyuan. Keywords: mitogenome, D-loop, rRNA gene, Dong Tao breed chicken, Gallus gallus domesticus Dong Tao chicken is an indigenous and rare breed of the Vietnamese chicken, mainly rearing in Khoai Chau district, Hung Yen province of Vietnam. The Dong Tao chicken breed has the imposing figure, healthy body and stout legs covered with reddish scales. The chicken is far more expensive than other Vietnamese native chicken because of high demand for its meat, which is considered as delicious and nutritious traditional food. The blood sample of Dong Tao chicken breed (DT347) was collected from Khoai-Chau District, Hung-Yen Province, Vietnam and stored in the Biobank of National Institute of Animal Husbandry, Vietnam. The genomic DNA was extracted from blood tissue using method as described (Sambrook, Russell, 2001). A set of primers was designed according to the report (Nishibori et al., 2001) to amplify and sequence complete mitochondrial genome. SeqScape 3.0 software (Thermo Fisher Scientific Inc.) was used to analyze mitochondrial DNA sequence. The distribution of all genes in the genome was analyzed by using transfer RNA (tRNA) Scan-SE 1.21 (Lowe, Eddy 1997) and MITOS tool (Bernt et al., 2013). The complete mitochondrial sequence of Dong Tao chicken has been deposited in GenBank with accession number KY094500. The entire mitogenome of Dong Tao chicken breed of 16,783 bp in length was obtained, with the nucleotide composition of A (30.29%), T (23.75%), C (32.48%), and G (13.48%). The mitogenome contained a non-coding control region (D-loop), 2 rRNA genes, 13 protein-coding genes, and 22 tRNA genes, which are similar to those of other reported fowls (Snyder et al., 2015, Xie et al., 2016, Yan et al., 2016, Zhang et al., 2016). Most of mitochondrial genes were located on the H-strand, except 8 tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Pro and tRNA-Glu) and ND6 gene, which are similar to the typical mitogenome of vertebrates (Boore, 1999, Snyder et al., 2015). The initiation codon for 12 of 13 mitochondrial genome proteins was ATG except the initiation codon of COX1 was GTG. The stop codon for ND1, COX2, ATPase8, ATPase6, ND3, ND4L, ND5, CytB and ND6 was TAA, while the stop codons for ND2 and COX1 were TAG and AGG, respectively. An incomplete stop codon ‘‘T– –’’ was found for COX3 and ND4. These features are common among Nguyen Dang Ton et al. 590 vertebrate mitochondrial genomes (Anderson et al., 1981). We found one base insertion at position 10,956, but reading frame was presumably maintained by translational frameshift of RNA. The 12S and 16S ribosomal RNA genes were separated by tRNA-Val and located between the tRNA-Leu and tRNA-Phe. The deduced 22 tRNA genes were distributed in rRNA and protein-coding genes, ranging from 65 to 76 bp in size. D-loop region was 1231 bp in length. Table 1. Location of genes and elements on the mitochondrial genome of Dong Tao chicken breed. Genes and elements Position Length Strand Codon From To Start Stop tRNA-Phe 1233 1302 70 H 12S rRNA 1302 2277 976 H tRNA-Val 2277 2349 73 H 16S rRNA 2353 3971 1619 H tRNA-Leu 3973 4046 74 H NADH-dehydrogenase subunit 1 (ND1) 4056 5024 969 H ATG TAA tRNA-Ile 5031 5102 72 H tRNA-Gln 5108 5177 70 L tRNA-Met 5177 5245 69 H NADH-dehydrogenase subunit 2 (ND2) 5246 6280 1035 H ATG TAA tRNA-Trp 6285 6360 76 H tRNA-Ala 6367 6435 69 L tRNA-Asn 6439 6511 73 L tRNA-Cys 6513 6578 66 L tRNA-Tyr 6579 6648 70 L Cytochrome oxidase subunit 1 (COX1) 6659 8191 1533 H TGT AGG tRNA-Ser 8192 8266 75 L tRNA-Asp 8269 8337 69 H Cytochrome oxidase subunit 2 (COX2) 8339 8962 624 H ATG TAA tRNA-Lys 9023 9090 68 H ATPase subunit 8 (ATP8) 9092 9250 159 H ATG TAA ATPase subunit 6 (ATP6) 9247 9927 681 H ATG TAA Cytochrome oxidase subunit 3 (COX3) 9930 10713 784 H ATG T-- tRNA-Gly 10714 10782 69 H NADH-dehydrogenase subunit 3 (ND3) 10783 11131 348 H ATG TAA tRNA-Arg 11136 11203 68 H NADH-dehydrogenase subunit 4 light chain (ND4L) 11204 11497 294 H ATG TAA NADH-dehydrogenase subunit 4 (ND4) 11494 12871 1378 H ATG T-- tRNA-His 12872 12940 69 H tRNA-Ser 12941 13007 67 H tRNA-Leu 13008 13078 71 H NADH-dehydrogenase subunit 5 (ND5) 13079 14884 1806 H Cytochrome B (CytB) 14913 16037 1125 H ATG TAA tRNA-Thr 16047 16115 69 H tRNA-Pro 16116 16185 70 L NADH-dehydrogenase subunit 6 (ND6) 16195 16713 519 L ATG CAT Journal of Biotechnology 16(4): 589-593, 2018 591 tRNA-Glu 16716 16783 68 L Figure 1. Molecular phylogenetic analysis of the complete mitogenome of Dong Tao chicken breed and 15 other mitogenomes of Gallus genus by Maximum Likelihood method. Complete mitogenomes were downloaded from GenBank with accession number as follows: AP003323 (G. gallus bankiva), KP681581 (G. gallus breed Guangxi), GU261678 (G. gallus breed Gushi), GU261711 (G. gallus breed Nixi), KP742951 (G. gallus breed Rugao), KF981434 (G. gallus breed Taoyuan), DQ648776 (G. gallus breed Tibetan), GU261683 (G. gallus breed Tulufan), GU261676 (G. gallus breed Wuding), GU261677 (G. gallus breed Xianju), AP003322 (G. gallus gallus), GU261696 (G. gallus jabouillei), GU261709 (G. gallus murghi), AP003321 (G. gallus spadiceus), AP003324 (G. varius) The complete mitogenome sequence of Gallus gallus breed Dong Tao together with other 15 mitogenomes of G. gallus species and G. varius were used for phylogenetic analysis. The phylogenetic tree was conducted in MEGA7 (Kumar et al., 2016) by using the Maximum Likelihood method based on the Tamura-Nei model (Tamura, Nei 1993), with mitogenome of G. varius as an outgroup. Phylogenetic analysis revealed that Dong Tao chicken breed was sister-close to G. gallus breed Guangxi, and paraphyletic to G. spadiceus, S. jabouillei, and a range of Chinese indigenous, ie. breeds Rugao and Taoyuan. The result showed that Dong Tao chicken breed close related to the other G. gallus species, with the sister position of G. gallus breed Guangxi (Figure 1). Complete mitogenome was used to reconstruct the history of animal domestication, such as in cattle (Achilli et al., 2009, Achilli et al., 2008, Bonfiglio et al., 2010), pigs (Wu et al., 2007), chicken (Miao et al., 2013) and sheep (Lancioni et al., 2013). This is the first mitochondrial genome of the Dong Tao chicken, which is the native chicken of Vietnam, has been sequenced. The complete mtDNA data initially contributes to the study of the conservation of indigenous chicken breeds in Vietnam. Acknowledgements: We gratefully acknowledge Dr. Le Thi Thuy (National Institute of Animal Husbandry, Ministry of Agriculture and Rural development, Vietnam) for providing chicken sample. This study was funded by the Institute of Genome Research (IGR), Vietnam Academy of Science and Technology (VAST). REFERENCES Achilli A, Bonfiglio S, Olivieri A, Malusa A, Pala M, Hooshiar Kashani B, Perego UA, Ajmone-Marsan P, Liotta L, Semino O, Bandelt HJ, Ferretti L, Torroni A (2009) The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS One 4(6): e5753. Achilli A, Olivieri A, Pellecchia M, Uboldi C, Colli L, Al- Zahery N, Accetturo M, Pala M, Hooshiar Kashani B, Perego UA, Battaglia V, Fornarino S, Kalamati J, Nguyen Dang Ton et al. 592 Houshmand M, Negrini R, Semino O, Richards M, Macaulay V, Ferretti L, Bandelt HJ, Ajmone-Marsan P, Torroni A (2008) Mitochondrial genomes of extinct aurochs survive in domestic cattle. Current Biology 18(4): R157−158. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290(5806): 457−465. Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, Middendorf M, Stadler PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69(2): 313−319. Bonfiglio S, Achilli A, Olivieri A, Negrini R, Colli L, Liotta L, Ajmone-Marsan P, Torroni A, Ferretti L (2010) The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy? PLoS One 5(12): e15760. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27(8): 1767−1780. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33(7): 1870-1874. Lancioni H, Di Lorenzo P, Ceccobelli S, Perego UA, Miglio A, Landi V, Antognoni MT, Sarti FM, Lasagna E, Achilli A (2013) Phylogenetic relationships of three Italian merino-derived sheep breeds evaluated through a complete mitogenome analysis. PLoS One 8(9): e73712. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5): 955−964. Miao YW, Peng MS, Wu GS, Ouyang YN, Yang ZY, Yu N, Liang JP, Pianchou G, Beja-Pereira A, Mitra B, Palanichamy MG, Baig M, Chaudhuri TK, Shen YY, Kong QP, Murphy RW, Yao YG, Zhang YP (2013) Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity (Edinb) 110(3): 277−282. Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, Yasue H (2001) Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Animal Genet 32(6): 380- 385. Sambrook J, Russell DW (2001) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, Unitied States of America. Snyder JC, Mackaness CA, Sopher MR, Huber JP, Disantis EJ, Senecal AJ, Vaughn BP, Desantis RS, Tobelmann PE, Balauff NM, Barry PM, Show MD, Speering LH, Genareo CA, Brenner FJ, Ray DB (2015) The complete mitochondrial genome sequence of the Canada goose (Branta canadensis). Mitochondrial DNA 26(5): 672−673. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3): 512−526. Wu GS, Yao YG, Qu KX, Ding ZL, Li H, Palanichamy MG, Duan ZY, Li N, Chen YS, Zhang YP (2007) Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol 8(11): R245. Xie Z, Zhang Y, Xie L, Liu J, Deng X, Xie Z, Fan Q, Luo S (2016) The complete mitochondrial genome of the Jingxi duck (Anas platyrhynchos). Mitochondrial DNA A DNA Mapp Seq Anal 27(2): 809−810. Yan ML, Ding SP, Ye SH, Wang CG, He BL, Yuan ZD, Liu LL (2016) The complete mitochondrial genome sequence of the Daweishan Mini chicken. Mitochondrial DNA A DNA Mapp, Seq Anal 27(1): 138−139. Zhang Y, Xie Z, Xie L, Deng X, Xie Z, Huang L, Huang J, Zeng T (2016) Analysis of the Rongshui Xiang duck (Anseriformes, Anatidae, Anas) mitochondrial DNA. Mitochondrial DNA A DNA Mapp Seq Anal 27(3): 1867−1868. TRÌNH TỰ HOÀN CHỈNH HỆ GEN TY THỂ GIỐNG GÀ ĐÔNG TẢO (GALLUS GALLUS DOMESTICUS) CỦA VIỆT NAM Nguyễn Đăng Tôn, Nguyễn Hải Hà, Vũ Phương Nhung, Nguyễn Thị Thanh Hoa, Ma Thị Huyền Thương, Trần Thị Bích Ngọc, Nguyễn Thùy Dương, Nông Văn Hải Viện Nghiên cứu hệ gen, Viện Hàn lâm Khoa học và Công nghệ Việt Nam TÓM TẮT Sử dụng phương pháp PCR và giải trình tự Sanger, chúng tôi đã xác định trình tự hoàn chỉnh của DNA ty thể giống gà Đông Tảo (Gallus gallus domesticus). Trình tự hoàn chỉnh của genome ty thể của giống gà Đông Journal of Biotechnology 16(4): 589-593, 2018 593 Tảo có chiều dài là 16.783 bp, với tỷ lệ các base nito A, T, C, G tương ứng là 30,29%, 23,75%, 32,48% và 13,48%. Genome ty thể của gà Đông Tảo gồm vùng điều khiển (D-loop), 2 gen mã hóa rRNA, 13 gen mã hóa cho các protein và 22 gen mã hóa cho các tRNA. Phân tích cây phát sinh chủng loại đã chỉ ra rằng giống gà Đông Tảo có quan hệ rất gần gũi với giống gà G. gallus Guangxi và có quan hệ họ hàng xa với các loài G. spadiceus, S. jabouillei và một số giống gà bản địa của Trung Quốc như giống Rugao và Taoyuan. Từ khóa: mitogenome, D-loop, rRNA gene, gà Đông Tảo, Gallus gallus domesticus