Hostname: page-component-cd9895bd7-fscjk Total loading time: 0 Render date: 2024-12-23T07:49:57.221Z Has data issue: false hasContentIssue false
  • English
  • Français

New insights into mitogenomic phylogeny and copy number in eight indigenous sheep populations based on the ATP synthase and cytochrome c oxidase genes

Published online by Cambridge University Press:  16 November 2017

P. Xiao ,
L. L. Niu ,
Q. J. Zhao ,
X. Y. Chen ,
L. J. Wang ,
L. Li ,
H. P. Zhang ,
J. Z. Guo ,
H. Y. Xu  and
T. Zhong
P. Xiao
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
L. L. Niu
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Q. J. Zhao
Affiliation:
CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
X. Y. Chen
Affiliation:
Institute of Animal Science and Veterinary of Hebei Province, Baoding 071000, China
L. J. Wang
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
L. Li
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
H. P. Zhang
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
J. Z. Guo
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
H. Y. Xu
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
T. Zhong*
Affiliation:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
*
†E-mail: [email protected]
Get access

Abstract

The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.

Keywords

Ovis ariesmitochondrial coding geneslineages distributiongenetic distancenon-synonymous mutations
Type
Research Article
Information
animal , Volume 12 , Issue 7 , July 2018 , pp. 1341 - 1349
Copyright
© The Animal Consortium 2017 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

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 and Young, IG 1981. Sequence and organization of the human mitochondrial genome. Nature 290, 457–465.Google Scholar
Ballester, M, Castello, A, Ibanez, E, Sanchez, A and Folch, JM 2004. Real-time quantitative PCR-based system for determining transgene copy number in transgenic animals. Biotechniques 37, 610–613.Google Scholar
Bandelt, HJ, Forster, P and Rohl, A 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16, 37–48.Google Scholar
Behera, BK, Kunal, SP, Paria, P, Das, P, Meena, DK, Pakrashi, S, Sahoo, AK, Panda, D, Jena, J and Sharma, AP 2015. Genetic differentiation in Indian Major Carp, Cirrhinus mrigala (Hamilton, 1822) from Indian Rivers, as revealed by direct sequencing analysis of mitochondrial Cytochrome b region. Mitochondrial DNA 26, 334–336.Google Scholar
Camus, MF, Wolf, JB, Morrow, EH and Dowling, DK 2015. Single nucleotides in the mtDNA sequence modify mitochondrial molecular function and are associated with sex-specific effects on fertility and aging. Current Biology 25, 2717–2722.Google Scholar
Carneiro, M, Afonso, S, Geraldes, A, Garreau, H, Bolet, G, Boucher, S, Tircazes, A, Queney, G, Nachman, MW and Ferrand, N 2011. The genetic structure of domestic rabbits. Molecular Biology and Evolution 28, 1801–1816.Google Scholar
Chen, SY, Duan, ZY, Sha, T, Xiangyu, J, Wu, SF and Zhang, YP 2006. Origin, genetic diversity, and population structure of Chinese domestic sheep. Gene 376, 216–223.Google Scholar
Delrieu-Trottin, E, Mona, S, Maynard, J, Neglia, V, Veuille, M and Planes, S 2017. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Scientific Reports 7, 40519.Google Scholar
Excoffier, L and Lischer, HE 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564–567.Google Scholar
Ferguson-Miller, S and Babcock, GT 1996. Heme/copper terminal oxidases. Chemical Reviews 96, 2889–2908.Google Scholar
Hartmann, N, Reichwald, K, Wittig, I, Drose, S, Schmeisser, S, Luck, C, Hahn, C, Graf, M, Gausmann, U, Terzibasi, E, Cellerino, A, Ristow, M, Brandt, U, Platzer, M and Englert, C 2011. Mitochondrial DNA copy number and function decrease with age in the short-lived fish Nothobranchius furzeri . Aging Cell 10, 824–831.Google Scholar
Jiang, L, Zhang, S, Dong, C, Chen, B, Feng, J, Peng, W, Mahboob, S, Al-Ghanim, KA and Xu, P 2016. Genome-wide identification, phylogeny, and expression of fibroblast growth genes in common carp. Gene 578, 225–231.Google Scholar
Joy, L, Mohitha, C, Divya, PR, Gopalakrishnan, A, Basheer, VS and Jena, JK 2016. Weak genetic differentiation in cobia, Rachycentron canadum from Indian waters as inferred from mitochondrial DNA ATPase 6 and 8 genes. Mitochondrial DNA. Part A, DNA Mapping, Sequencing and Analysis 27, 2819–2821.Google Scholar
Kersten, B, Faivre Rampant, P, Mader, M, Le Paslier, MC, Bounon, R, Berard, A, Vettori, C, Schroeder, H, Leple, JC and Fladung, M 2016. Genome sequences of Populus tremula chloroplast and mitochondrion: implications for holistic poplar breeding. PLoS One 11, e0147209.Google Scholar
Kibegwa, FM, Githui, KE, Jung’a, JO, Badamana, MS and Nyamu, MN 2016. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya. Journal of Animal Breeding and Genetics 133, 238–247.Google Scholar
Liao, K, Yan, J, Mai, K and Ai, Q 2016. Dietary lipid concentration affects liver mitochondrial DNA copy number, gene expression and DNA methylation in large yellow croaker (Larimichthys crocea). Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology 193, 25–32.Google Scholar
Lv, FH, Peng, WF, Yang, J, Zhao, YX, Li, WR, Liu, MJ, Ma, YH, Zhao, QJ, Yang, GL, Wang, F, Li, JQ, Liu, YG, Shen, ZQ, Zhao, SG, Hehua, E, Gorkhali, NA, Farhad Vahidi, SM, Muladno, M, Naqvi, AN, Tabell, J, Iso-Touru, T, Bruford, MW, Kantanen, J, Han, JL and Li, MH 2015. Mitogenomic meta-analysis identifies two phases of migration in the history of Eastern Eurasian sheep. Molecular Biology and Evolution 32, 2515–2533.Google Scholar
Mahami-Oskouei, M, Kaseb-Yazdanparast, A, Spotin, A, Shahbazi, A, Adibpour, M, Ahmadpour, E and Ghabouli-Mehrabani, N 2016. Gene flow for Echinococcus granulosus metapopulations determined by mitochondrial sequences: a reliable approach for reflecting epidemiological drift of parasite among neighboring countries. Experimental Parasitology 171, 77–83.Google Scholar
Mason, IL 1984. Evolution of domesticated animals. Longman, London, New York.Google Scholar
Meadows, JR, Cemal, I, Karaca, O, Gootwine, E and Kijas, JW 2007. Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics 175, 1371–1379.Google Scholar
Meadows, JR, Hiendleder, S and Kijas, JW 2011. Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel. Heredity (Edinb) 106, 700–706.Google Scholar
Niemi, M, Blauer, A, Iso-Touru, T, Harjula, J, Nystrom Edmark, V, Rannamae, E, Lougas, L, Sajantila, A, Liden, K and Taavitsainen, JP 2015. Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses. PLoS One 10, e0123821.Google Scholar
Nijtmans, LG, Klement, P, Houstek, J and van den Bogert, C 1995. Assembly of mitochondrial ATP synthase in cultured human cells: implications for mitochondrial diseases. Biochimica et Biophysica Acta 1272, 190–198.Google Scholar
Niu, L, Chen, X, Xiao, P, Zhao, Q, Zhou, J, Hu, J, Sun, H, Guo, J, Li, L, Wang, L, Zhang, H and Zhong, T 2016. Detecting signatures of selection within the Tibetan sheep mitochondrial genome. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis 28, 1–9.Google Scholar
Pedrosa, S, Uzun, M, Arranz, JJ, Gutierrez-Gil, B, San Primitivo, F and Bayon, Y 2005. Evidence of three maternal lineages in near Eastern sheep supporting multiple domestication events. Proceedings. Biological Sciences 272, 2211–2217.Google Scholar
Rak, M, Benit, P, Chretien, D, Bouchereau, J, Schiff, M, El-Khoury, R, Tzagoloff, A and Rustin, P 2016. Mitochondrial cytochrome c oxidase deficiency. Clinical Science 130, 393–407.Google Scholar
Ramadan, HA and El-Hefnawi, MM 2008. Phylogenetic analysis and comparison between cow and buffalo (including Egyptian buffaloes) mitochondrial displacement-loop regions. Mitochondrial DNA 19, 401–410.Google Scholar
Resende, A, Goncalves, J, Muigai, AW and Pereira, F 2016. Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya. Animal Genetics 47, 377–381.Google Scholar
Rozas, J 2009. DNA sequence polymorphism analysis using DnaSP. Methods in Molecular Biology 537, 337–350.Google Scholar
Sperl, W, Jesina, P, Zeman, J, Mayr, JA, Demeirleir, L, VanCoster, R, Pickova, A, Hansikova, H, Houst’kova, H, Krejcik, Z, Koch, J, Smet, J, Muss, W, Holme, E and Houstek, J 2006. Deficiency of mitochondrial ATP synthase of nuclear genetic origin. Neuromuscular Disorders 16, 821–829.Google Scholar
Tamura, K, Peterson, D, Peterson, N, Stecher, G, Nei, M and Kumar, S 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739.CrossRefGoogle ScholarPubMed
Wang, Y, Shen, Y, Feng, C, Zhao, K, Song, Z, Zhang, Y, Yang, L and He, S 2016. Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude. Scientific Reports 6, 29690.Google Scholar
Workalemahu, T, Enquobahrie, DA, Tadesse, MG, Hevner, K, Gelaye, B, Sanchez, SE and Williams, MA 2017. Genetic variations related to maternal whole blood mitochondrial DNA copy number: a genome-wide and candidate gene study. Journal of Maternal–Fetal & Neonatal Medicine 30, 1–7.Google Scholar
Yuan, Y, Wang, W, Li, H, Yu, Y, Tao, J, Huang, S and Zeng, Z 2015. Nonsense and missense mutation of mitochondrial ND6 gene promotes cell migration and invasion in human lung adenocarcinoma. BMC Cancer 15, 346.Google Scholar
Zeder, MA 2008. Domestication and early agriculture in the Mediterranean Basin: origins, diffusion, and impact. Proceedings of National Academy of Sciences USA 105, 11597–11604.Google Scholar
Supplementary material: Image

Xiao et al supplementary material

Figure S1

Download Xiao et al supplementary material(Image)
Image 30.9 KB
Supplementary material: Image

Xiao et al supplementary material

Figure S2

Download Xiao et al supplementary material(Image)
Image 144.7 KB
Supplementary material: Image

Xiao et al supplementary material

Figure S3

Download Xiao et al supplementary material(Image)
Image 131.8 KB
Supplementary material: File

Xiao et al supplementary material

Table S1

Download Xiao et al supplementary material(File)
File 55.8 KB
Supplementary material: File

Xiao et al supplementary material

Table S2

Download Xiao et al supplementary material(File)
File 164.4 KB
Supplementary material: File

Xiao et al supplementary material

Table S3

Download Xiao et al supplementary material(File)
File 50.7 KB
Supplementary material: File

Xiao et al supplementary material

Table S4

Download Xiao et al supplementary material(File)
File 27.6 KB
Supplementary material: File

Xiao et al supplementary material

Table S5

Download Xiao et al supplementary material(File)
File 73.2 KB
Supplementary material: File

Xiao et al supplementary material

Table S6

Download Xiao et al supplementary material(File)
File 38.9 KB