Heteroplasmy in the complete chicken mitochondrial genome


Autoři: Yanqun Huang aff001;  Weiwei Lu aff001;  Jiefei Ji aff001;  Xiangli Zhang aff001;  Pengfei Zhang aff001;  Wen Chen aff001
Působiště autorů: College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China aff001
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224677

Souhrn

Chicken mitochondrial DNA is a circular molecule comprising ~16.8 kb. In this study, we used next-generation sequencing to investigate mitochondrial heteroplasmy in the whole chicken mitochondrial genome. Based on heteroplasmic detection thresholds at the 0.5% level, 178 cases of heteroplasmy were identified in the chicken mitochondrial genome, where 83% were due to nucleotide transitions. D-loop regionwas hot spot region for mtDNA heteroplasmy in the chicken since 130 cases of heteroplasmy were located in these regions. Heteroplasmy varied among intraindividual tissues with allele-specific, position-specific, and tissue-specific features. Skeletal muscle had the highest abundance of heteroplasmy. Cases of heteroplasmy at mt.G8682A and mt.G16121A were validated by PCR-restriction fragment length polymorphism analysis, which showed that both had low ratios of heteroplasmy occurrence in five natural breeds. Polymorphic sites were easy to distinguish. Based on NGS data for crureus tissues, mitochondrial mutation/heteroplasmy exhibited clear maternal inheritance features at the whole mitochondrial genomic level. Further investigations of the heterogeneity of the mt.A5694T and mt.T5718G transitions between generations using pyrosequencing based on pedigree information indicated that the degree of heteroplasmy and the occurrence ratio of heteroplasmy decreased greatly from the F0 to F1 generations in the mt.A5694T and mt.T5718G site. Thus, the intergenerational transmission of heteroplasmy in chicken mtDNA exhibited a rapid shift toward homoplasmy within a single generation. Our findings indicate that heteroplasmy is a widespread phenomenon in chicken mitochondrial genome, in which most sites exhibit low heteroplasmy and the allele frequency at heteroplasmic sites changes significantly during transmission events. It suggests that heteroplasmy may be under negative selection to some degree in the chicken.

Klíčová slova:

Alleles – Chicken models – Chickens – Mitochondria – Mitochondrial DNA – Next-generation sequencing – Polymerase chain reaction – Heteroplasmy


Zdroje

1. Desjardins P, Morais R. Sequence and gene organization of the chicken mitochondrial genome:A novel gene order in higher vertebrates. Journal of Molecular Biology. 1990;212(4):599–634. doi: 10.1016/0022-2836(90)90225-B 2329578

2. Stewart JB, Chinnery PF. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nature reviews: Genetics. 2015;16(9):530–42. doi: 10.1038/nrg3966 26281784

3. Moslemi AR, Tulinius M, Holme E, Oldfors A. Threshold expression of the tRNA Lys A8344G mutation in single muscle fibres. Neuromuscular Disorders. 1998;8(5):345–9. doi: 10.1016/s0960-8966(98)00029-7 9673990

4. Rohlin A, Wernersson J, Engwall Y, Wiklund L, Björk J, Nordling M. Parallel sequencing used in detection of mosaic mutations: comparison with four diagnostic DNA screening techniques. Human Mutation. 2009;30(6):1012–20. doi: 10.1002/humu.20980 19347965

5. Bai RK, Wong LJC. Detection and quantification of heteroplasmic mutant mitochondrial DNA by real-time amplification refractory mutation system quantitative PCR analysis: a single-step approach. Clinical chemistry. 2004;50(6):996–1001. doi: 10.1373/clinchem.2004.031153 15073091

6. White HE, Durston VJ, Seller A, Fratter C, Harvey JF, Cross NC. Accurate detection and quantitation of heteroplasmic mitochondrial point mutations by pyrosequencing. Genetic Testing. 2005;9(3):190. doi: 10.1089/gte.2005.9.190 16225398

7. He Y, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, Velculescu VE, et al. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature. 2010;464(7288):610–4. doi: 10.1038/nature08802 20200521

8. Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. American Journal of Human Genetics. 2010;87(2):237–49. doi: 10.1016/j.ajhg.2010.07.014 20696290

9. Tang S, Huang T. Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. BioTechniques. 2010;48(4):287–96. doi: 10.2144/000113389 20569205

10. Rensch T, Villar D, Horvath J, Odom DT, Flicek P. Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data. Genome biology. 2016;17(1):139. doi: 10.1186/s13059-016-0996-y 27349964

11. Giuliani C, Barbieri C, Li M, Bucci L, Monti D, Passarino G, et al. Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing. Aging (Albany NY). 2014;6(6):454–67.

12. Holland MM, Mcquillan MR, O’Hanlon KA. Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy. Croatian Medical Journal. 2011;52(3):299–313. doi: 10.3325/cmj.2011.52.299 21674826

13. Guo Y, Li CI, Sheng Q, Winther JF, Cai Q, Boice JD, et al. Very Low-Level Heteroplasmy mtDNA Variations Are Inherited in Humans. Journal of genetics and genomics. 2013;40(12):607–15. doi: 10.1016/j.jgg.2013.10.003 24377867

14. Lu WW, Hou LL, Zhang WW, Zhang PF, Chen W, Kang X, et al. Study on heteroplasmic variation and the effect of chicken mitochondrial ND2. Mitochondrial DNA Part A 2016;27(4):2303–9.

15. Cagnone G, Tsai TS, Srirattana K, Rossello F, Powell DR, Rohrer G, et al. Segregation of Naturally Occurring Mitochondrial DNA Variants in a Mini-pig Model. Genetics. 2016;202:931–44. doi: 10.1534/genetics.115.181321 26819245

16. Spicer AM, Kun TJ, Sacks BN, Wictum EJ. Mitochondrial DNA sequence heteroplasmy levels in domestic dog hair. Forensic Sci Int Genet. 2014;11:7–12. doi: 10.1016/j.fsigen.2014.02.006 24631692

17. Wu J, Smith RK, Freeman AE, Beitz DC, McDaniel BT, Lindberg GL. Sequence heteroplasmy of D-loop and rRNA coding regions in mitochondrial DNA from Holstein cows of independent maternal lineages. Biochemical genetics. 2000;38(9–10):323–35. doi: 10.1023/a:1002061101697 11129526

18. Zhang W, Cui H, Wong LJ. Comprehensive 1-Step Molecular Analyses of Mitochondrial Genome by Massively Parallel Sequencing. Clinical chemistry. 2012;58(9):1322–31. doi: 10.1373/clinchem.2011.181438 22777720

19. Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–60. doi: 10.1093/bioinformatics/btp324 19451168

20. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. doi: 10.1093/bioinformatics/btp352 19505943

21. Pereira S, Baker A. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evolutionary Biology. 2004;4(1):17.

22. Santibanez-Koref M, Griffin H, Turnbull DM, Chinnery PF, Herbert M, Hudson G. Assessing mitochondrial heteroplasmy using next generation sequencing: A note of caution. Mitochondrion. 2019;46:302–6. doi: 10.1016/j.mito.2018.08.003 30098421

23. Cui H, Li F, Chen D, Wang G, Truong CK, Enns GM, et al. Comprehensive next-generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders. Genetics in Medicine. 2013;15(5):388–94. doi: 10.1038/gim.2012.144 23288206

24. Ye F, Samuels DC, Clark T, Guo Y. High-throughput sequencing in mitochondrial DNA research. Mitochondrion. 2014;17:157–63. doi: 10.1016/j.mito.2014.05.004 24859348

25. Li M, Schroder R, Ni S, Madea B, Stoneking M. Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(8):2491–6. doi: 10.1073/pnas.1419651112 25675502

26. Ramos A, Santos C, Mateiu L, Gonzalez Mdel M, Alvarez L, Azevedo L, et al. Frequency and pattern of heteroplasmy in the complete human mitochondrial genome. PloS one. 2013;8(10):e74636. doi: 10.1371/journal.pone.0074636 24098342

27. Naue J, Horer S, Sanger T, Strobl C, Hatzer-Grubwieser P, Parson W, et al. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion. 2015;20:82–94. doi: 10.1016/j.mito.2014.12.002 25526677

28. Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic acids research. 2012;40(Web Server issue):W452–7. doi: 10.1093/nar/gks539 22689647

29. Luo S, Valencia CA, Zhang J, Lee NC, Slone J, Gui B, et al. Biparental Inheritance of Mitochondrial DNA in Humans. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(51):13039–44. doi: 10.1073/pnas.1810946115 30478036

30. Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, et al. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biology. 2011;12(6):R59. doi: 10.1186/gb-2011-12-6-r59 21699709

31. Wai T, Teoli D, Shoubridge EA. The mitochondrial DNA genetic bottleneck results from replication of a subpopulation of genomes. Nature genetics. 2008;40(12):1484–8. doi: 10.1038/ng.258 19029901

32. Yin T, Wang J, Xiang H, Pinkert CA, Li Q, Zhao X. Dynamic characteristics of the mitochondrial genome in SCNT pigs. Biological chemistry. 2019;400(5):613–23. doi: 10.1515/hsz-2018-0273 30367779

33. Rebolledo-Jaramillo B, Su MS-W, Stoler N, McElhoe JA, Dickins B, Blankenberg D, et al. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences, USA. 2014;111(43):15474–9.


Článek vyšel v časopise

PLOS One


2019 Číslo 11