- Volume 30 Issue 7
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The complete mitochondrial genome sequence of the indigenous I pig (Sus scrofa) in Vietnam
- Nguyen, Hieu Duc (Institute of Genome Research, Vietnam Academy of Science and Technology) ;
- Bui, Tuan Anh (Institute of Forensic Science) ;
- Nguyen, Phuong Thanh (Institute of Genome Research, Vietnam Academy of Science and Technology) ;
- Kim, Oanh Thi Phuong (Institute of Genome Research, Vietnam Academy of Science and Technology) ;
- Vo, Thuy Thi Bich (Institute of Genome Research, Vietnam Academy of Science and Technology)
- Received : 2016.08.11
- Accepted : 2016.12.13
- Published : 2017.07.01
Objective: The I pig is a long nurtured longstanding breed in Vietnam, and contains excellent indigenous genetic resources. However, after 1970s, I pig breeds have become a small population because of decreasing farming areas and increasing pressure from foreign breeds with a high growth rate. Thus, there is now the risk of the disappearance of the I pigs breed. The aim of this study was to focus on classifying and identifying the I pig genetic origin and supplying molecular makers for conservation activities. Methods: This study sequenced the complete mitochondrial genome and used the sequencing result to analyze the phylogenetic relationship of I pig with Asian and European domestic pigs and wild boars. The full sequence was annotated and predicted the secondary tRNA. Results: The total length of I pig mitochondrial genome (accession number KX094894) was 16,731 base pairs, comprised two rRNA (12S and 16S), 22 tRNA and 13 mRNA genes. The annotation structures were not different from other pig breeds. Some component indexes as AT content, GC, and AT skew were counted, in which AT content (60.09%) was smaller than other pigs. We built the phylogenetic trees from full sequence and D loop sequence using Bayesian method. The result showed that I pig, Banna mini, wild boar (WB) Vietnam and WB Hainan or WB Korea, WB Japan were a cluster. They were a group within the Asian clade distinct from Chinese pigs and other Asian breeds in both phylogenetic trees (0.0004 and 0.0057, respectively). Conclusion: These results were similar to previous phylogenic study in Vietnamese pig and showed the genetic distinctness of I pig with other Asian domestic pigs.
Complete Mitochondrial Genome;Genetic Distance;Mitochondrial DNA;I Pig;Phylogenetic Relationships
Supported by : Vietnam National Foundation for Science and Technology Development (NAFOSTED)
- Dang-Nguyen TQ, Tich NK, Nguyen BX, et al. Introduction of various Vietnamese indigenous pig breeds and their conservation by using assisted reproductive techniques. J Reprod Dev 2010;56:31-5. https://doi.org/10.1262/jrd.09-165K
- Phung TV. Livestock technique of reproductive sow. 1st Hanoi, Vietnam: Labour Publishing House; 2005.
- Bruford MW, Bradley DG, Luikart G. DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 2003;4:900-10. https://doi.org/10.1038/nrg1203
- Giles RE, Blanc H, Cann HM, Wallace DC. Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci USA 1980;77: 6715-9. https://doi.org/10.1073/pnas.77.11.6715
- Wolstenholme DR. Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 1992;141:173-216.
- Brown WM, George M, Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 1979;76:1967-71. https://doi.org/10.1073/pnas.76.4.1967
- Boore JL. Animal mitochondrial genomes. Nucleic Acids Res 1999;27: 1767-80. https://doi.org/10.1093/nar/27.8.1767
- Kim KI, Lee JH, Li K, et al. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim Genet 2002;33:19-25. https://doi.org/10.1046/j.1365-2052.2002.00784.x
- Toro MA, Rodriganez J, Silio L, Rodriguez C. Genealogical analysis of a closed herd of black hairless Iberian pigs. Conserv Biol 2000;14: 1843-51. https://doi.org/10.1046/j.1523-1739.2000.99322.x
- Sambrook J, Russell DW. Molecular cloning: a laboratory manual. 3rd ed. New York, US: Coldspring-Harbour Laboratory Press; 2001.
- Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J Hered 2001;92:371-3. https://doi.org/10.1093/jhered/92.4.371
- Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792-7. https://doi.org/10.1093/nar/gkh340
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30: 2725-9. https://doi.org/10.1093/molbev/mst197
- Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012;29: 1969-73. https://doi.org/10.1093/molbev/mss075
- Sun JL, Zhang B, Ma QY, et al. Analysis of mtDNA Partial D-loop Sequences in Luchuan Pig. Zhongguo Xu Mu Shou Yi 2010;6:035.
- Li M, Jin L, Ma J, et al. Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs. Mitochondrial DNA Part A DNA Mapp Seq Anal 2016;27:747-52.
- Ghivizzani SC, Mackay SL, Madsen CS, Laipis PJ, Hauswirth WW. Transcribed heteroplasmic repeated sequences in the porcine mitochondrial DNA D-loop region. J Mol Evol 1993;37:36-47.
- Hassanin A, Leger N, Deutsch J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst Biol 2005;54:277-98. https://doi.org/10.1080/10635150590947843
- Wei S-J, Shi M, Chen X-X, et al. New views on strand asymmetry in insect mitochondrial genomes. PLoS ONE 2010;5:e12708. https://doi.org/10.1371/journal.pone.0012708
- Giuffra E, Kijas J, Amarger V, Carlborg O, Jeon J-T, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 2000;154:1785-91.
- Fernandez A, Alves E, Ovilo C, Rodriguez M, Silio L. Divergence time estimates of East Asian and European pigs based on multiple near complete mitochondrial DNA sequences. Anim Genet 2011;42: 86-8. https://doi.org/10.1111/j.1365-2052.2010.02068.x
- Lan H, Shi L. The origin and genetic differentiation of native breeds of pigs in southwest China: an approach from mitochondrial DNA polymorphism. Biochem Genet 1993;31:51-60. https://doi.org/10.1007/BF02399819
- Hongo H, Ishiguro N, Watanobe T, et al. Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian domestic pigs and Ryukyu wild boars. Zool Sci 2002;19:1329-35. https://doi.org/10.2108/zsj.19.1329