Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers
Autoři:
Findley R. Finseth aff001; Thomas C. Nelson aff001; Lila Fishman aff001
Působiště autorů:
Division of Biological Sciences, University of Montana, Missoula Montana, United States of America
aff001; Keck Science Department, Claremont-McKenna, Scripps, and Pitzer Colleges, Claremont California, United States of America
aff002
Vyšlo v časopise:
Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers. PLoS Genet 17(4): e1009418. doi:10.1371/journal.pgen.1009418
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1009418
Souhrn
Centromeres are essential mediators of chromosomal segregation, but both centromeric DNA sequences and associated kinetochore proteins are paradoxically diverse across species. The selfish centromere model explains rapid evolution by both components via an arms-race scenario: centromeric DNA variants drive by distorting chromosomal transmission in female meiosis and attendant fitness costs select on interacting proteins to restore Mendelian inheritance. Although it is clear than centromeres can drive and that drive often carries costs, female meiotic drive has not been directly linked to selection on kinetochore proteins in any natural system. Here, we test the selfish model of centromere evolution in a yellow monkeyflower (Mimulus guttatus) population polymorphic for a costly driving centromere (D). We show that the D haplotype is structurally and genetically distinct and swept to a high stable frequency within the past 1500 years. We use quantitative genetic mapping to demonstrate that context-dependence in the strength of drive (from near-100% D transmission in interspecific hybrids to near-Mendelian in within-population crosses) primarily reflects variable vulnerability of the non-driving competitor chromosomes, but also map an unlinked modifier of drive coincident with kinetochore protein Centromere-specific Histone 3 A (CenH3A). Finally, CenH3A exhibits a recent (<1000 years) selective sweep in our focal population, implicating local interactions with D in ongoing adaptive evolution of this kinetochore protein. Together, our results demonstrate an active co-evolutionary arms race between DNA and protein components of the meiotic machinery in Mimulus, with important consequences for individual fitness and molecular divergence.
Klíčová slova:
Centromeres – Evolutionary genetics – Gene mapping – Genomics – Haplotypes – Heterozygosity – Population genetics – Quantitative trait loci
Zdroje
1. Malik H, Henikoff S. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics. 2001;157: 1293–1298. 11238413
2. Henikoff S, Ahmad K, Malik H. The centromere paradox: stable inheritance with rapidly evolving DNA. Science. 2001;293: 1098–1102. doi: 10.1126/science.1062939 11498581
3. Finseth FR, Dong Y, Saunders A, Fishman L. Duplication and Adaptive Evolution of a Key Centromeric Protein in Mimulus, a Genus with Female Meiotic Drive. Mol Biol Evol. 2015;32: 2694–2706. doi: 10.1093/molbev/msv145 26104011
4. Malik H, Henikoff S. Conflict begets complexity: the evolution of centromeres. Curr Opin Genet Dev. 2002;12: 711–718. doi: 10.1016/s0959-437x(02)00351-9 12433586
5. Kursel LE, Malik H. The cellular mechanisms and consequences of centromere drive. Curr Opin Cell Biol. 2018;52: 58–65. doi: 10.1016/j.ceb.2018.01.011 29454259
6. McLaughlin RN, Malik H. Genetic conflicts: the usual suspects and beyond. J Exp Biol. 2017;220: 6–17. doi: 10.1242/jeb.148148 28057823
7. Lampson MA, Black BE. Cellular and molecular mechanisms of centromere drive. Cold Spring Harb Symp Quant Biol. 2017;82: 249–257. doi: 10.1101/sqb.2017.82.034298 29440567
8. Zhang W, Mao J-H, Zhu W, Jain AK, Liu K, Brown JB, et al. Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy. Nature Comm. 2016;7: 12619. doi: 10.1038/ncomms12619 27577169
9. Ravi M, Chan SWL. Haploid plants produced by centromere-mediated genome elimination. Nature. 2010;464: 615–618. doi: 10.1038/nature08842 20336146
10. Akera T, Chmátal L, Trimm E, Yang K, Aonbangkhen C, Chenoweth DM, et al. Spindle asymmetry drives non-Mendelian chromosome segregation. Science. American Association for the Advancement of Science; 2017;358: 668–672. doi: 10.1126/science.aan0092 29097549
11. Chmátal L, Gabriel SI, Mitsainas GP, Martínez-Vargas J, Ventura J, Searle JB, et al. Centromere strength provides the cell biological basis for meiotic drive and karyotype evolution in mice. Curr Biol. 2014;24: 2295–2300. doi: 10.1016/j.cub.2014.08.017 25242031
12. Fishman L, Kelly JK. Centromere-associated meiotic drive and female fitness variation in Mimulus. Evolution. 2015;69: 1208–1218. doi: 10.1111/evo.12661 25873401
13. Fishman L, Willis JH. A novel meiotic drive locus almost completely distorts segregation in Mimulus (monkeyflower) hybrids. Genetics. 2005;169: 347–353. doi: 10.1534/genetics.104.032789 15466426
14. Fishman L, Saunders A. Centromere-associated female meiotic drive entails male fitness costs in monkeyflowers. Science. 2008;322: 1559–1562. doi: 10.1126/science.1161406 19056989
15. Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 2013;14: R10. doi: 10.1186/gb-2013-14-1-r10 23363705
16. Malik H. Mimulus finds centromeres in the driver’s seat. Trends Ecol Evol. 2005;20: 151–154. doi: 10.1016/j.tree.2005.01.014 16701359
17. Troth A, Puzey JR, Kim RS, Willis JH, Kelly JK. Selective trade-offs maintain alleles underpinning complex trait variation in plants. Science. 2018;361: 475–478. doi: 10.1126/science.aat5760 30072534
18. Crow JF. Why is Mendelian segregation so exact? Bioessays. Wiley Online Library; 1991;13: 305–312. doi: 10.1002/bies.950130609 1909864
19. Flagel LE, Blackman BK, Fishman L, Monnahan PJ, Sweigart A, Kelly JK. GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity. Feltus FA, editor. PLoS Comput Biol. 2019;15: e1006949. doi: 10.1371/journal.pcbi.1006949 30986215
20. Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL. Speciation and introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genetics. 2014;10: e1004410. doi: 10.1371/journal.pgen.1004410 24967630
21. Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW. Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Nat Acad Sci USA. 2000;97: 7360–7365. doi: 10.1073/pnas.97.13.7360 10861004
22. Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Nat Acad Sci USA. National Academy of Sciences; 1979;76: 5269–5273. doi: 10.1073/pnas.76.10.5269 291943
23. Monnahan PJ, Kelly JK. The genomic architecture of flowering time varies across space and time in Mimulus guttatus. Genetics. Genetics; 2017;206: 1621–1635. doi: 10.1534/genetics.117.201483 28455350
24. Puzey JR, Willis JH, Kelly JK. Population structure and local selection yield high genomic variation in Mimulus guttatus. Mol Ecol. 2017;26: 519–535. doi: 10.1111/mec.13922 27859786
25. Larracuente AM, Presgraves DC. The selfish Segregation Distorter gene complex of Drosophila melanogaster. Genetics. 2012;192: 33–53. doi: 10.1534/genetics.112.141390 22964836
26. Dawe R, Lowry EG, Gent JI, Stitzer MC, Swentowsky KW, Higgins DM, et al. A Kinesin-14 motor activates neocentromeres to promote meiotic drive in maize. Cell. Elsevier Inc; 2018;173: 1–30. doi: 10.1016/j.cell.2018.03.012 29570990
27. Le Goff S, Keçeli BN, Jeřábková H, Heckmann S, Rutten T, Cotterell S, et al. The H3 histone chaperone NASPSIM3 escorts CenH3 in Arabidopsis. Plant J. John Wiley & Sons, Ltd; 2020;101: 71–86. doi: 10.1111/tpj.14518 31463991
28. Zheng T, Nibau C, Phillips DW, Jenkins G, Armstrong SJ, Doonan JH. CDKG1 protein kinase is essential for synapsis and male meiosis at high ambient temperature in Arabidopsis thaliana. Proc Nat Acad Sci USA. 2014;111: 2182–2187. doi: 10.1073/pnas.1318460111 24469829
29. Sweigart AL, Brandvain Y, Fishman L. Making a murderer: the evolutionary framing of hybrid gamete-killers. Trends Genet. 2019;35: 245–252. doi: 10.1016/j.tig.2019.01.004 30826132
30. Fishman L, Sweigart AL. When two rights make a wrong: the evolutionary genetics of plant hybrid incompatibilities. Annu Rev Plant Biol. 2018;69: 701–737. doi: 10.1146/annurev-arplant-042817-040113 29505737
31. Burt A, Trivers R. Selfish DNA and breeding system in flowering plants. Proc R Soc Lond B. 1998;265: 141–146.
32. Scoville AG, Lee YW, Willis JH, Kelly JK. Contribution of chromosomal polymorphisms to the G-matrix of Mimulus guttatus. New Phytol. 2009;183: 803–815. doi: 10.1111/j.1469-8137.2009.02947.x 19659590
33. Maheshwari S, Tan EH, West A, Franklin FCH, Comai L, Chan SWL. Naturally occurring differences in CENH3 affect chromosome segregation in zygotic mitosis of hybrids. Bomblies K, editor. PLoS Genetics. Public Library of Science; 2015;11: e1004970. doi: 10.1371/journal.pgen.1004970 25622028
34. Hall DW, Dawe R. Modeling the evolution of female meiotic drive in maize. G3. G3: Genes, Genomes, Genetics; 2018;8: 123–130. doi: 10.1534/g3.117.300073 29122849
35. Flagel LE, Willis JH, Vision TJ. The standing pool of genomic structural variation in a natural population of Mimulus guttatus. Genome Biol Evol. 2014;6: 53–64. doi: 10.1093/gbe/evt199 24336482
36. Lee YW, Fishman L, Kelly JK, Willis JH. A segregating inversion generates fitness variation in yellow monkeyflower (Mimulus guttatus). Genetics. Genetics; 2016;202: 1473–1484. doi: 10.1534/genetics.115.183566 26868767
37. Case AL, Finseth FR, Barr CM, Fishman L. Selfish evolution of cytonuclear hybrid incompatibility in Mimulus. Proc R Soc Lond B. The Royal Society; 2016;283: 20161493. doi: 10.1098/rspb.2016.1493 27629037
38. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114–2120. doi: 10.1093/bioinformatics/btu170 24695404
39. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25: 1754–1760. doi: 10.1093/bioinformatics/btp324 19451168
40. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25: 2078–2079. doi: 10.1093/bioinformatics/btp352 19505943
41. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 20644199
42. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 2011;43: 491–498. doi: 10.1038/ng.806 21478889
43. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27: 2156–2158. doi: 10.1093/bioinformatics/btr330 21653522
44. Holeski LM, Monnahan P, Koseva B, McCool N, Lindroth RL, Kelly JK. A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation. G3. Genetics Society of America; 2014;4: 813–821. doi: 10.1534/g3.113.010124 24626287
45. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215: 403–410. doi: 10.1016/S0022-2836(05)80360-2 2231712
46. Nelson TC, Monnahan PJ, McIntosh MK, Anderson K, Waltz EM, Finseth FR, et al. Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers. Mol Ecol. John Wiley & Sons, Ltd (10.1111); 2018;107: 321. doi: 10.1111/mec.14904 30346101
47. Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ. PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol Biol Evol. 2014;31: 1929–1936. doi: 10.1093/molbev/msu136 24739305
48. Harrell FE Jr. Hmisc: Harrell Miscellaneous, R Package 4.1–1 [Internet]. 4 ed. 2018. Available: https://github.com/harrelfe/Hmisc
49. Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. Nature Publishing Group; 2011;475: 493–496. doi: 10.1038/nature10231 21753753
50. Sweigart AL, Fishman L, Willis JH. A simple genetic incompatibility causes hybrid male sterility in Mimulus. Genetics. 2006;172: 2465–2479. doi: 10.1534/genetics.105.053686 16415357
51. Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, et al. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 2011;21: 610–617. doi: 10.1101/gr.115402.110 21233398
52. Fishman L, Kelly AJ, Morgan E, Willis JH. A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics. 2001;159: 1701–1716. 11779808
53. Fishman L, Willis JH, Wu CA, Lee YW. Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae). Heredity. 2014;112: 562–568. doi: 10.1038/hdy.2013.143 24398885
54. Wang S, Basten CJ, Zeng Z-B. Windows QTL Cartographer 2.5. Dept. of Statistics, North Carolina State Univ; 2005.
55. SAS Institute. JMP version 14. 14 ed. Cary, NC: SAS Institute; 2018.
56. Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007;81: 1084–1097. doi: 10.1086/521987 17924348
57. Sweigart AL, Flagel LE. Evidence of natural selection acting on a polymorphic hybrid incompatibility locus in Mimulus. Genetics. 2015;199: 543–554. doi: 10.1534/genetics.114.171819 25428983
58. Garner AG, Kenney AM, Fishman L, Sweigart AL. Genetic loci with parent-of-origin effects cause hybrid seed lethality in crosses between Mimulus species. New Phytol. 2016;211: 319–331. doi: 10.1111/nph.13897 26924810
Článek vyšel v časopise
PLOS Genetics
2021 Číslo 4
- Distribuce a lokalizace speciálně upravených exosomů může zefektivnit léčbu svalových dystrofií
- Prof. Jan Škrha: Metformin je bezpečný, ale je třeba jej bezpečně užívat a léčbu kontrolovat
- FDA varuje před selfmonitoringem cukru pomocí chytrých hodinek. Jak je to v Česku?
- Masturbační chování žen v ČR − dotazníková studie
- O krok blíže k pochopení efektu placeba při léčbě bolesti
Nejčtenější v tomto čísle
- Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions
- Functional assessment of the “two-hit” model for neurodevelopmental defects in Drosophila and X. laevis
- Pathways and signatures of mutagenesis at targeted DNA nicks
- Using genetic variants to evaluate the causal effect of cholesterol lowering on head and neck cancer risk: A Mendelian randomization study