Parent-progeny sequencing indicates higher mutation rates in heterozygotes

Nature

Volumn 523, Issue 7561, 2015, Pages 463-467

  Yang, Sihai ^a   Wang, Long ^a   Huang, Ju ^a   Zhang, Xiaohui ^a   Yuan, Yang ^a   Chen, Jian Qun ^a   Hurst, Laurence D ^b   Tian, Dacheng ^a  

^a NANJING UNIVERSITY   (China)

^b Milner Centre for Evolution   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DICOTYLEDON; GENOME; HETEROZYGOSITY; HONEYBEE; INTRASPECIFIC INTERACTION; MUTATION; PHYSIOLOGICAL RESPONSE; RECOMBINATION; RICE;

ARABIDOPSIS; ARTICLE; BALANCING SELECTION; HETEROZYGOTE; HOMOZYGOTE; MUTATION RATE; NONHUMAN; PARENT; PLANT GENOME; PRIORITY JOURNAL; PROGENY; PURIFYING SELECTION; ANIMAL; ARTIFACT; BEE; CROSSING OVER; DNA SEQUENCE; FEMALE; GENETIC SELECTION; GENETICS; GENOME; GENOMICS; MALE; MEIOSIS; MULTIGENE FAMILY; MUTAGENESIS; PEDIGREE; RICE; SINGLE NUCLEOTIDE POLYMORPHISM;

APIS MELLIFERA; ARABIDOPSIS;

ANIMALS; ARABIDOPSIS; ARTIFACTS; BEES; CROSSING OVER, GENETIC; FEMALE; GENOME; GENOMICS; HETEROZYGOTE; HOMOZYGOTE; MALE; MEIOSIS; MULTIGENE FAMILY; MUTAGENESIS; MUTATION RATE; ORYZA SATIVA; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84937884710     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14649     Document Type: Article

References (43)

1. Hodgkinson, A. Eyre-Walker, A. Variation in themutation rate acrossmammalian genomes. Nature Rev. Genet. 12, 756-766 (2011).
2. Chen, X. and Zhang, J. No gene-specific optimization ofmutation rate in Escherichia coli. Mol. Biol. Evol. 30, 1559-1562 (2013).
3. Chuang, J. H. and Li, H. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol. 2, e29 (2004).
4. Martincorena, I., Seshasayee, A. S. N. and Luscombe, N. M. Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature 485, 95-98 (2012).
5. Roach, J. C. et al. Analysis of genetic inheritance in a family quartet by wholegenome sequencing. Science 328, 636-639 (2010).
6. Wang, J., Fan, H. C., Behr, B. and Quake, S. R. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150, 402-412 (2012).
7. Sung, W., Ackerman, M. S., Miller, S. F., Doak, T. G. and Lynch, M. Drift-barrier hypothesis and mutation-rate evolution. Proc. Natl Acad. Sci. USA 109, 18488-18492 (2012).
8. Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92-94 (2010).
9. Jiang, C. et al. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Res. 24, 1821-1829 (2014).
10. Cutter, A. D. and Payseur, B. A. Genomic signatures of selection at linked sites: unifying the disparity among species. Nature Rev. Genet. 14, 262-274 (2013).
11. Lercher,M. J. and Hurst, L. D. Human SNP variability andmutation rate are higher in regions of high recombination. Trends Genet. 18, 337-340 (2002).
12. Magni, G. E. and Borstel, R. C. V. Different rates of spontaneous mutation during mitosis and meiosis in yeast. Genetics 47, 1097-1108 (1962).
13. Perry, J. and Ashworth, A. Evolutionary rate of a gene affected by chromosomal position. Curr. Biol. 9, 987 (1999).
14. Pratto, F. et al. Recombination initiation maps of individual human genomes. Science 346, 1256442 (2014).
15. Rattray, A., Santoyo, G., Shafer, B. and Strathern, J. N. Elevated mutation rate during meiosis in Saccharomyces cerevisiae. PLoS Genet. 11, e1004910 (2015).
16. Arbeithuber, B., Betancourt, A. J., Ebner, T. and Tiemann-Boege, I. Crossovers are associated withmutation and biased gene conversion at recombination hotspots. Proc. Natl Acad. Sci. USA 112, 2109-2114 (2015).
17. Liu, H. et al. Causes and consequences of crossing-over evidenced via a highresolution recombinational landscape of the honey bee. Genome Biol. 16, 15 (2015).
18. Amos, W. Heterozygosity and mutation rate: evidence for an interaction and its implications. Bioessays 32, 82-90 (2010).
19. Hollister, J. D., Ross-Ibarra, J. and Gaut, B. S. Indel-associated mutation rate varies with mating system in flowering plants. Mol. Biol. Evol. 27, 409-416 (2010).
20. Amos, W. Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence? Proc. R. Soc. Lond. B 277, 1443-1449 (2010).
21. Tian, D. et al. Single-nucleotide mutation rate increases close to insertions/ deletions in eukaryotes. Nature 455, 105-108 (2008).
22. Pal, C., Macia, M. D., Oliver, A., Schachar, I. and Buckling, A. Coevolution with viruses drives the evolution of bacterial mutation rates. Nature 450, 1079-1081 (2007).
23. Cox, E. C. On the organization of higher chromosomes. Nature New Biol. 239, 133-134 (1972).
24. Shee, C., Gibson, J. L. and Rosenberg, S. M. Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli. Cell Rep. 2, 714-721 (2012).
25. Pál, C. and Hurst, L. D. Evidence for co-evolution of gene order and recombination rate. Nature Genet. 33, 392-395 (2003).
26. Gladyshev, E. and Kleckner, N. Direct recognition of homology between double helices of DNA in Neurospora crassa. Nature Commun. 5, 3509 (2014).
27. Boateng, K. A., Bellani, M. A., Gregoretti, I. V., Pratto, F. and Camerini-Otero, R. D. Homologous pairing preceding SPO11-mediated double-strand breaks in mice. Dev. Cell 24, 196-205 (2013).
28. Malkova, A. and Haber, J. E. Mutations arising during repair of chromosome breaks. Annu. Rev. Genet. 46, 455-473 (2012).
29. Ichijima, Y. et al. MDC1 directs chromosome-wide silencing of the sex chromosomes in male germ cells. Genes Dev. 25, 959-971 (2011).
30. Cao, J. et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genet. 43, 956-963 (2011).
31. Gao, Z.-Y. et al. Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc. Natl Acad. Sci. USA 110, 14492-14497 (2013).
32. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWAMEM. Preprint at http://arxiv.org/abs/1303.3997 (2013).
33. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491-498 (2011).
34. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
35. Ghoneim, D. H., Myers, J. R., Tuttle, E. and Paciorkowski, A. R. Comparison of insertion/deletion calling algorithms on human next-generation sequencing data. BMC Res. Notes 7, 864 (2014).
36. Thorvaldsdóttir, H., Robinson, J. T. and Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178-192 (2013).
37. Li, M. and Stoneking, M. A new approach for detecting low-level mutations in nextgeneration sequence data. Genome Biol. 13, R34 (2012).
38. Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 29472948 (2007).
39. Keightley, P. D., Ness, R. W., Halligan, D. L. and Haddrill, P. R. Estimation of the spontaneousmutation rate pernucleotide site in a Drosophilamelanogaster full-sib family. Genetics 196, 313-320 (2014).
40. Frazer, K. A., Pachter, L., Poliakov, A., Rubin, E. M. and Dubchak, I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32, W273-W279 (2004).
41. Yang, Z. PAML4: Phylogenetic Analysis byMaximumLikelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
42. R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2013).
43. North, B. V., Curtis, D. and Sham, P. C. A note on the calculation of empirical P values from Monte Carlo procedures. Am. J. Hum. Genet. 72, 498-499 (2003).