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Lee SI, Kim NS. Transposable elements and genome size variations in plants. Genomics Inform. 2014;12(3):87-97doi: 10.5808/GI.2014.12.3.87.
Lee, S. I., & Kim, N. S. (2014). Transposable elements and genome size variations in plants. Genomics & informatics, 12(3), 87-97. https://doi.org/10.5808/GI.2014.12.3.87
Lee, Sung-Il, and Kim, Nam-Soo. "Transposable elements and genome size variations in plants." Genomics & informatics vol. 12,3 (2014): 87-97. doi: https://doi.org/10.5808/GI.2014.12.3.87
Lee SI, Kim NS. Transposable elements and genome size variations in plants. Genomics Inform. 2014 Sep;12(3):87-97. doi: 10.5808/GI.2014.12.3.87. Epub 2014 Sep 30. PMID: 25317107; PMCID: PMC4196380.
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Genomics Inform. 2014 Sep;12(3):87-97. doi: 10.5808/GI.2014.12.3.87. Epub 2014 Sep 30.

Transposable elements and genome size variations in plants.

Genomics & informatics

Sung-Il Lee, Nam-Soo Kim

Affiliations

  1. Department of Molecular Bioscience, Kangwon National University, Chuncheon 200-701, Korea.

PMID: 25317107 PMCID: PMC4196380 DOI: 10.5808/GI.2014.12.3.87

Abstract

Although the number of protein-coding genes is not highly variable between plant taxa, the DNA content in their genomes is highly variable, by as much as 2,056-fold from a 1C amount of 0.0648 pg to 132.5 pg. The mean 1C-value in plants is 2.4 pg, and genome size expansion/contraction is lineage-specific in plant taxonomy. Transposable element fractions in plant genomes are also variable, as low as ~3% in small genomes and as high as ~85% in large genomes, indicating that genome size is a linear function of transposable element content. Of the 2 classes of transposable elements, the dynamics of class 1 long terminal repeat (LTR) retrotransposons is a major contributor to the 1C value differences among plants. The activity of LTR retrotransposons is under the control of epigenetic suppressing mechanisms. Also, genome-purging mechanisms have been adopted to counter-balance the genome size amplification. With a wealth of information on whole-genome sequences in plant genomes, it was revealed that several genome-purging mechanisms have been employed, depending on plant taxa. Two genera, Lilium and Fritillaria, are known to have large genomes in angiosperms. There were twice times of concerted genome size evolutions in the family Liliaceae during the divergence of the current genera in Liliaceae. In addition to the LTR retrotransposons, non-LTR retrotransposons and satellite DNAs contributed to the huge genomes in the two genera by possible failure of genome counter-balancing mechanisms.

Keywords: C-value; DNA transposable elements; LTR retrotransposons; genome size; genome-purging

References

  1. Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19916-21 - PubMed
  2. Curr Opin Genet Dev. 1995 Dec;5(6):814-21 - PubMed
  3. Science. 2006 Oct 6;314(5796):119-21 - PubMed
  4. Genetics. 1941 Mar;26(2):234-82 - PubMed
  5. Brief Funct Genomics. 2014 Jul;13(4):308-17 - PubMed
  6. Plant Cell. 2000 May;12(5):617-36 - PubMed
  7. Nucleic Acids Res. 2007 Jan;35(Database issue):D332-8 - PubMed
  8. J Evol Biol. 2007 Nov;20(6):2296-308 - PubMed
  9. Plant J. 2003 Apr;34(2):249-55 - PubMed
  10. Ann Bot. 2005 Apr;95(5):789-97 - PubMed
  11. Nat Commun. 2013;4:1595 - PubMed
  12. Science. 1968 Aug 9;161(3841):529-40 - PubMed
  13. Plant J. 2011 Apr;66(1):58-65 - PubMed
  14. Proc Natl Acad Sci U S A. 1989 Jul;86(13):5015-9 - PubMed
  15. Nature. 2013 May 30;497(7451):579-84 - PubMed
  16. Ann Bot. 2011 Feb;107(2):255-68 - PubMed
  17. Genome. 2013 Sep;56(9):495-503 - PubMed
  18. BMC Genomics. 2007 Jul 06;8:218 - PubMed
  19. Plant Mol Biol. 1993 Aug;22(5):829-46 - PubMed
  20. Curr Biol. 2003 Mar 4;13(5):421-6 - PubMed
  21. Science. 2009 Nov 20;326(5956):1112-5 - PubMed
  22. Science. 1966 Nov 11;154(3750):791-4 - PubMed
  23. BMC Genomics. 2010 Jul 07;11:420 - PubMed
  24. Ann Bot. 2005 Jan;95(1):177-90 - PubMed
  25. Nat Rev Genet. 2005 Jan;6(1):24-35 - PubMed
  26. BMC Mol Biol. 2008 Aug 11;9:73 - PubMed
  27. Gene. 2007 Apr 1;390(1-2):166-74 - PubMed
  28. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1411-5 - PubMed
  29. Nature. 1980 Apr 17;284(5757):604-7 - PubMed
  30. Genome Res. 2009 Aug;19(8):1419-28 - PubMed
  31. Genome Biol Evol. 2013;5(4):723-33 - PubMed
  32. Genome Res. 2006 Oct;16(10):1262-9 - PubMed
  33. Bioessays. 2006 Sep;28(9):913-22 - PubMed
  34. Nat Genet. 2011 May;43(5):476-81 - PubMed
  35. Mol Biol Evol. 2012 Feb;29(2):849-59 - PubMed
  36. Genome Biol Evol. 2013;5(5):954-65 - PubMed
  37. Genomics Inform. 2012 Dec;10(4):226-33 - PubMed
  38. Mol Gen Genet. 1993 Feb;237(1-2):97-104 - PubMed
  39. BMC Evol Biol. 2006 Aug 16;6:62 - PubMed
  40. Genetics. 2004 Oct;168(2):1009-18 - PubMed
  41. Genome Res. 2007 May;17(5):594-601 - PubMed
  42. Genetica. 2000;108(1):57-72 - PubMed
  43. Nature. 2013 Jun 6;498(7452):94-8 - PubMed
  44. BMC Plant Biol. 2010 Nov 30;10:265 - PubMed
  45. Genome Res. 2004 May;14(5):860-9 - PubMed
  46. Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2322-7 - PubMed
  47. Nat Rev Genet. 2007 Apr;8(4):272-85 - PubMed
  48. Plant Cell. 1994 Jun;6(6):907-16 - PubMed
  49. Nature. 2009 Oct 22;461(7267):1130-4 - PubMed
  50. Trends Biochem Sci. 2012 Nov;37(11):477-83 - PubMed
  51. Nat Genet. 2005 Sep;37(9):997-1002 - PubMed
  52. Trends Genet. 2002 Nov;18(11):547-50 - PubMed
  53. Plant Cell. 1997 Sep;9(9):1509-1514 - PubMed
  54. Nat Struct Mol Biol. 2005 Aug;12(8):715-21 - PubMed
  55. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17620-5 - PubMed
  56. Annu Rev Genet. 2007;41:331-68 - PubMed
  57. Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17811-6 - PubMed
  58. Trends Genet. 1989 Apr;5(4):103-7 - PubMed
  59. Science. 2012 Nov 9;338(6108):758-67 - PubMed
  60. Ann Bot. 2005 Jan;95(1):255-60 - PubMed
  61. Genome Biol. 2004;5(6):225 - PubMed
  62. Plant Cell. 1992 Oct;4(10):1283-94 - PubMed
  63. Ann Bot. 2011 Mar;107(3):467-590 - PubMed
  64. Heredity (Edinb). 2006 Dec;97(6):381-8 - PubMed
  65. Mol Cell Biol. 1994 Mar;14(3):1613-25 - PubMed
  66. Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):9068-73 - PubMed
  67. Cytogenet Genome Res. 2005;109(1-3):90-103 - PubMed
  68. Genome Res. 2002 Jul;12(7):1075-9 - PubMed
  69. Annu Rev Genet. 1971;5:237-56 - PubMed
  70. Nat Commun. 2010 Sep 21;1:77 - PubMed
  71. Proc Natl Acad Sci U S A. 1942 Nov;28(11):458-63 - PubMed
  72. Genome. 2005 Dec;48(6):1120-6 - PubMed
  73. Plant Cell. 2004 Apr;16(4):794-803 - PubMed
  74. Evolution. 2002 Feb;56(2):233-52 - PubMed
  75. Nat Rev Genet. 2007 Dec;8(12):973-82 - PubMed
  76. Genome Biol Evol. 2013;5(10):1886-901 - PubMed
  77. Nature. 1980 Apr 17;284(5757):601-3 - PubMed
  78. Genetics. 1941 Sep;26(5):542-71 - PubMed

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