OpenLB
Open Library of Bioscience
Advanced Search
Biomolecules
Feb 27, 2025;15 (3):

Transposable Element Landscape in the Monotypic Species (Hance) Krass (Melastomataceae) and Its Role in Ecological Adaptation.

Wei Wu, Yuan Zeng, Zecheng Huang, Huiting Peng, Zhanghai Sun, Bin Xu
Author Information
  1. Wei Wu: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China. ORCID
  2. Yuan Zeng: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
  3. Zecheng Huang: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
  4. Huiting Peng: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
  5. Zhanghai Sun: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
  6. Bin Xu: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China.
PMID: 40149882 DOI: 10.3390/biom15030346

Abstract

Transposable elements (TEs) are crucial for genome evolution and ecological adaptation, but their dynamics in non-model plants are poorly understood. Using genomic, transcriptomic, and population genomic approaches, we analyzed the TE landscape of (Melastomataceae), a species distributed across tropical and subtropical southern China. We identified 64,866 TE copies (16.76% of a 235 Mb genome), dominated by Ty3/Gypsy retrotransposons (8.82%) and DNA/Mutator elements (2.7%). A genome-wide analysis revealed 13 TE islands enriched in genes related to photosynthesis, tryptophan metabolism, and stress response. We identified 3859 high-confidence TE insertion polymorphisms (TIPs), including 29 fixed insertions between red and white flower ecotypes, affecting genes involved in cell wall modification, stress response, and secondary metabolism. A transcriptome analysis of the flower buds identified 343 differentially expressed TEs between the ecotypes, 30 of which were near or within differentially expressed genes. The non-random distribution (primarily within 5 kb of genes) and association with adaptive traits suggest a significant role in 's successful colonization of diverse habitats. Our findings provide insights into how TEs contribute to plant genome evolution and ecological adaptation in tropical forests, particularly through their influence on regulatory networks governing stress response and development.

Keywords

Barthea barthei TE insertion polymorphisms ecological adaptation genome evolution transposable elements

References

  1. Nature. 2013 May 30;497(7451):579-84 [PMID: 23698360]
  2. Mol Plant. 2021 Aug 2;14(8):1244-1265 [PMID: 34216829]
  3. Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33 [PMID: 25431634]
  4. Nat Genet. 2006 May;38(5):594-7 [PMID: 16642024]
  5. Plant Cell Rep. 2020 Sep;39(9):1161-1174 [PMID: 32435866]
  6. Annu Rev Plant Biol. 2009;60:43-66 [PMID: 19007329]
  7. Nature. 2004 Sep 30;431(7008):569-73 [PMID: 15457261]
  8. Mob DNA. 2017 Dec 6;8:19 [PMID: 29225705]
  9. Plant J. 2014 Dec;80(6):937-50 [PMID: 25292417]
  10. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10 [PMID: 15240870]
  11. Nat Commun. 2014 Dec 16;5:5495 [PMID: 25510865]
  12. Bioinformatics. 2020 Aug 1;36(15):4269-4275 [PMID: 32415954]
  13. PLoS One. 2021 Oct 27;16(10):e0251713 [PMID: 34705830]
  14. J Integr Plant Biol. 2008 Sep;50(9):1130-9 [PMID: 18844781]
  15. Adv Biophys. 2004;38:141-59 [PMID: 15493332]
  16. Front Plant Sci. 2019 Mar 12;10:290 [PMID: 30915095]
  17. Front Plant Sci. 2021 Jan 28;11:615942 [PMID: 33584756]
  18. J Exp Bot. 2021 May 18;72(11):4132-4143 [PMID: 33606874]
  19. Mol Biol Evol. 2013 Apr;30(4):772-80 [PMID: 23329690]
  20. Science. 2009 Nov 20;326(5956):1112-5 [PMID: 19965430]
  21. Elife. 2016 Jun 03;5: [PMID: 27258693]
  22. Nucleic Acids Res. 2015 Jan;43(Database issue):D222-6 [PMID: 25414356]
  23. Genome Res. 2010 Sep;20(9):1297-303 [PMID: 20644199]
  24. Biochim Biophys Acta. 2012 Feb;1819(2):86-96 [PMID: 21867785]
  25. Curr Opin Plant Biol. 2022 Feb;65:102140 [PMID: 34883307]
  26. Bioinformatics. 2014 May 1;30(9):1312-3 [PMID: 24451623]
  27. Bioinformatics. 2014 Aug 1;30(15):2114-20 [PMID: 24695404]
  28. Mob DNA. 2020 Jul 27;11:28 [PMID: 32742313]
  29. Methods Mol Biol. 2021;2250:157-169 [PMID: 33900602]
  30. Annu Rev Genet. 2020 Nov 23;54:539-561 [PMID: 32955944]
  31. Plant J. 2014 Nov;80(4):582-91 [PMID: 25182777]
  32. Plant J. 2019 Dec;100(5):1052-1065 [PMID: 31381222]
  33. Plant J. 2008 May;54(3):481-95 [PMID: 18266919]
  34. Cell. 2024 Dec 26;187(26):7603-7620.e22 [PMID: 39667937]
  35. Nature. 2014 Feb 6;506(7486):85-8 [PMID: 24463522]
  36. Mol Ecol. 2013 Mar;22(6):1503-17 [PMID: 23293987]
  37. Nat Commun. 2013;4:2301 [PMID: 23934508]
  38. Mol Biol Evol. 2020 Jan 1;37(1):291-294 [PMID: 31432070]
  39. Curr Opin Plant Biol. 2018 Apr;42:23-29 [PMID: 29453028]
  40. Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9589-94 [PMID: 23696664]
  41. Plant Physiol. 2023 Feb 12;191(2):1122-1137 [PMID: 36494195]
  42. Front Plant Sci. 2024 May 01;15:1365686 [PMID: 38751846]
  43. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14728-33 [PMID: 26553984]
  44. Nat Commun. 2019 Apr 2;10(1):1494 [PMID: 30940818]
  45. Nature. 2013 Jun 6;498(7452):94-8 [PMID: 23665961]
  46. Curr Opin Plant Biol. 2004 Aug;7(4):465-71 [PMID: 15231271]
  47. Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16969-74 [PMID: 24089449]
  48. New Phytol. 2020 Aug;227(3):698-713 [PMID: 32242934]
  49. Sci China Life Sci. 2016 Jan;59(1):24-37 [PMID: 26753674]
  50. PLoS Genet. 2021 Oct 14;17(10):e1009768 [PMID: 34648488]
  51. Elife. 2016 Dec 02;5: [PMID: 27911260]
  52. Nat Rev Genet. 2020 Dec;21(12):721-736 [PMID: 32576954]
  53. Nat Rev Genet. 2013 Jan;14(1):49-61 [PMID: 23247435]
  54. Trends Ecol Evol. 2016 Jul;31(7):514-526 [PMID: 27080578]
  55. Appl Plant Sci. 2017 Apr 11;5(4): [PMID: 28439476]
  56. BMC Evol Biol. 2015 Apr 22;15:69 [PMID: 25896861]
  57. Genome Biol. 2018 Dec 13;19(1):216 [PMID: 30541598]
  58. Annu Rev Genet. 2007;41:331-68 [PMID: 18076328]
  59. Plant J. 2004 Dec;40(6):968-78 [PMID: 15584961]
  60. Trends Genet. 1989 Apr;5(4):103-7 [PMID: 2543105]
  61. Bioinformatics. 2013 Jan 1;29(1):15-21 [PMID: 23104886]
  62. Plant Cell. 2016 Feb;28(2):304-13 [PMID: 26869697]
  63. BMC Plant Biol. 2016 Jun 29;16(1):148 [PMID: 27358074]
  64. Am J Hum Genet. 2007 Sep;81(3):559-75 [PMID: 17701901]
  65. Brief Bioinform. 2021 Nov 5;22(6): [PMID: 34050351]
  66. Plant Cell. 2012 Mar;24(3):1242-55 [PMID: 22427337]
  67. Genome Biol. 2019 Dec 16;20(1):275 [PMID: 31843001]
  68. Mol Plant. 2010 Jan;3(1):2-20 [PMID: 20035037]
  69. Nat Commun. 2015 Sep 21;6:8326 [PMID: 26387805]
  70. Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13751-2 [PMID: 26556885]
  71. Bioinformatics. 2015 Nov 15;31(22):3593-9 [PMID: 26206304]
  72. Nat Rev Genet. 2007 Dec;8(12):973-82 [PMID: 17984973]
  73. New Phytol. 2006;171(3):469-99 [PMID: 16866954]
  74. Mob DNA. 2019 Jan 03;10:1 [PMID: 30622655]
  75. Annu Rev Genet. 2012;46:21-42 [PMID: 22905872]
  76. Plant J. 2003 Nov;36(4):522-31 [PMID: 14617082]
  77. Nucleic Acids Res. 2021 Jul 2;49(W1):W317-W325 [PMID: 34086934]
  78. Nature. 2009 Oct 22;461(7267):1135-8 [PMID: 19847267]

Grants

  1. 2020KJCX002/Science and Technology Program from Forestry Administration of Guangdong Province

MeSH Term

DNA Transposable Elements
Adaptation, Physiological
Genome, Plant
Gene Expression Regulation, Plant
Transcriptome
Evolution, Molecular
Flowers

Chemicals

DNA Transposable Elements
Journal Article
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.0TEgenomegeneselementsTEsevolutionecologicaladaptationidentifiedstressresponseTransposablegenomicMelastomataceaetropicalanalysismetabolisminsertionpolymorphismsflowerecotypesdifferentiallyexpressedwithincrucialdynamicsnon-modelplantspoorlyunderstoodUsingtranscriptomicpopulationapproachesanalyzedlandscapespeciesdistributedacrosssubtropicalsouthernChina64866copies1676%235MbdominatedTy3/Gypsyretrotransposons882%DNA/Mutator27%genome-widerevealed13islandsenrichedrelatedphotosynthesistryptophan3859high-confidenceTIPsincluding29fixedinsertionsredwhiteaffectinginvolvedcellwallmodificationsecondarytranscriptomebuds34330nearnon-randomdistributionprimarily5kbassociationadaptivetraitssuggestsignificantrole'ssuccessfulcolonizationdiversehabitatsfindingsprovideinsightscontributeplantforestsparticularlyinfluenceregulatorynetworksgoverningdevelopmentElementLandscapeMonotypicSpeciesHanceKrassRoleEcologicalAdaptationBartheabartheitransposable

Similar Articles

Cited By