Genome Stability and Evolution: Attempting a Holistic View

Trends in Plant Science

Volumn 21, Issue 9, 2016, Pages 749-757

  Schubert, Ingo ^a   Vu, Giang T H ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

DNA double strand break repair; Genome size evolution; Genome stability; Karyotype evolution; Whole genome duplication

Indexed keywords

DOUBLE STRANDED DNA BREAK; GENE DUPLICATION; GENETICS; GENOMIC INSTABILITY; MOLECULAR EVOLUTION; PLANT GENOME;

DNA BREAKS, DOUBLE-STRANDED; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, PLANT; GENOMIC INSTABILITY;

EID: 84978877973     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2016.06.003     Document Type: Review

References (55)

1. 1 Thomas, C.A., The genetic organization of chromosomes. Annu. Rev. Genet 5 (1971), 237–256.
2. 2 Gregory, T.R., Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. Camb. Philos. Soc. 76 (2001), 65–101.
3. 3 Bennett, M.D., Leitch, I.J., Nuclear DNA amounts in angiosperms: progress, problems and prospects. Ann. Bot. 95 (2005), 45–90.
4. 4 Stelzer, C.P., et al. Genome size evolution at the speciation level: the cryptic species complex Brachionus plicatilis (Rotifera). BMC Evol. Biol., 11, 2011, 90.
5. 5 Ellis, L.L., et al. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. PLoS Genet., 10, 2014, e1004522.
6. 6 Smarda, P., Bures, P., Understanding intraspecific variation in genome size in plants. Preslia 82 (2010), 41–61.
7. 7 Realini, M.F., et al. Intra-specific variation in genome size in maize: cytological and phenotypic correlates. AoB Plants, 8, 2015, plv138.
8. 8 Schubert, I., et al. DNA damage processing and aberration formation in plants. Cytogenet. Genome Res. 104 (2004), 104–108.
9. 9 Lieber, M.R., The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 79 (2010), 181–211.
10. 10 San Filippo, J., et al. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 77 (2008), 229–257.
11. 11 Shrivastav, M., et al. Regulation of DNA double-strand break repair pathway choice. Cell Res. 18 (2008), 134–147.
12. 12 Moore, J.K., Haber, J.E., Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383 (1996), 644–646.
13. 13 Petrov, D.A., et al. High intrinsic rate of DNA loss in Drosophila. Nature 384 (1996), 346–349.
14. 14 Devos, K.M., et al. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12 (2002), 1075–1079.
15. 15 Hu, T.T., et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43 (2011), 476–481.
16. 16 Kirik, A., et al. Species-specific double-strand break repair and genome evolution in plants. EMBO J. 19 (2000), 5562–5566.
17. 17 Puchta, H., The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J. Exp. Bot. 56 (2005), 1–14.
18. 18 Vu, G.T.H., et al. Comparative genome analysis reveals divergent genome size evolution in a carnivorous plant genus. Plant Genome, 2015, 10.3835/plantgenome2015.04.0021 Published online October 21, 2015.
19. 19 Orel, N., Puchta, H., Differences in the processing of DNA ends in Arabidopsis thaliana and tobacco: possible implications for genome evolution. Plant Mol. Biol. 51 (2003), 523–531.
20. 20 Zhang, H., et al. A cell cycle-dependent BRCA1–UHRF1 cascade regulates DNA double-strand break repair pathway choice. Nat. Commun., 7, 2016, 10201.
21. 21 Yun, M.H., Hiom, K., CtIP-BRCA1 modulates the choice of DNA double-strand-break repair pathway throughout the cell cycle. Nature 459 (2009), 460–463.
22. 22 Schubert, I., Lysak, M.A., Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet. 27 (2011), 207–216.
23. 23 Hedges, D.J., Deininger, P.L., Inviting instability: transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat. Res. 616 (2007), 46–59.
24. 24 Fawcett, J.A., et al. Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol. Biol. Evol. 29 (2012), 849–859.
25. 25 Fawcett, J.A., et al. Plants with double genomes might have had a better chance to survive the Cretaceous–Tertiary extinction event. Proc. Natl Acad. Sci. U.S.A. 106 (2009), 5737–5742.
26. 26 Geiser, C., et al. Repeated whole-genome duplication, karyotype reshuffling, and biased retention of stress-responding genes in Buckler mustard. Plant Cell 28 (2016), 17–27.
27. 27 Tran, T.D., et al. Chromatin organization and cytological features of carnivorous Genlisea species with large genome size differences. Front. Plant Sci., 6, 2015, 613.
28. 28 Schubert, I., Alteration of chromosome numbers by generation of minichromosomes–is there a lower limit of chromosome size for stable segregation?. Cytogenet. Cell Genet. 93 (2001), 175–181.
29. 29 Voss, S.R., et al. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Res. 21 (2011), 1306–1312.
30. 30 Birchler, J.A., Han, F., Meiotic behavior of small chromosomes in maize. Front. Plant Sci., 4, 2013, 505.
31. 31 Lysak, M.A., et al. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl Acad. Sci. U.S.A. 103 (2006), 5224–5229.
32. 32 Mandakova, T., Lysak, M.A., Chromosomal phylogeny and karyotype evolution in x = 7 crucifer species (Brassicaceae). Plant Cell 20 (2008), 2559–2570.
33. 33 Mandakova, T., et al. Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22 (2010), 2277–2290.
34. 34 Schubert, I., Rieger, R., A new mechanism for altering chromosome number during karyotype evolution. Theor. Appl. Genet. 70 (1985), 213–221.
35. 35 Yang, F., et al. A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma 103 (1995), 642–652.
36. 36 Schubert, I., Oud, J.L., There is an upper limit of chromosome size for normal development of an organism. Cell 88 (1997), 515–520.
37. 37 Hudakova, S., et al. Barley chromosome arms longer than half of the spindle axis interfere with nuclear divisions. Cytogenet. Genome Res. 98 (2002), 101–107.
38. 38 Schubert, I., et al. Unscheduled apoptosis in meristematic plant cells is triggered via terminal deletions in artificially elongated chromosome arms. Theor. Appl. Genet. 96 (1998), 1022–1026.
39. 39 Bennett, M.D., Nuclear DNA content and minimum generation time in herbaceous plants. Proc. Biol. Sci. 181 (1972), 109–135.
40. 40 Petrov, D.A., Evolution of genome size: new approaches to an old problem. Trends Genet. 17 (2001), 23–28.
41. 41 Leitch, I.J., et al. The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann. Bot. 101 (2008), 805–814.
42. 42 Kelly, L.J., et al. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytol. 208 (2015), 596–607.
43. 43 Nystedt, B., et al. The Norway spruce genome sequence and conifer genome evolution. Nature 497 (2013), 579–584.
44. 44 Kalendar, R., et al. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl Acad. Sci. U.S.A. 97 (2000), 6603–6607.
45. 45 Clark, J., et al. Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. New Phytol. 210 (2016), 1072–1082.
46. 46 Freeling, M., et al. A solution to the C-value paradox and the function of junk DNA: the genome balance hypothesis. Mol. Plant 8 (2015), 899–910.
47. 47 Navratilova, A., et al. Karyotype analysis of four Vicia species using in situ hybridization with repetitive sequences. Ann. Bot. 91 (2003), 921–926.
48. 48 Schubert, I., Rieger, R., Alteration by centric fission of the diploid chromosome-number in Vicia faba L. Genetica 81 (1990), 67–69.
49. 49 Bures, P., et al. Holocentric chromosomes. Leitch, I.J., et al. (eds.) Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, 2012, Springer, 187–208.
50. 50 Sullivan, W., et al. Delays in anaphase initiation occur in individual nuclei of the syncytial Drosophila embryo. Mol. Biol. Cell 4 (1993), 885–896.
51. 51 Greilhuber, J., et al. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol. (Stuttg.) 8 (2006), 770–777.
52. 52 Tran, T.D., et al. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. Plant J. 84 (2015), 1087–1099.
53. 53 Vu, G.T., et al. Repair of site-specific DNA double-strand breaks in barley occurs via diverse pathways primarily involving the sister chromatid. Plant Cell 26 (2014), 2156–2167.
54. 54 Leitch, A.R., Leitch, I.J., Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol. 194 (2012), 629–646.
55. 55 Li, Z., et al. Early genome duplications in conifers and other seed plants. Sci. Adv., 1, 2015, e1501084.