Angiosperms are unique among land plant lineages in the occurrence of key genes in the RNA-Directed DNA methylation (RdDM) Pathway

Genome Biology and Evolution

Volumn 7, Issue 9, 2015, Pages 2648-2662

  Ma, Lu ^a   Hatlen, Andrea ^a   Kelly, Laura J ^a   Becher, Hannes ^a   Wang, Wencai ^a   Kovarik, Ales ^b   Leitch, Ilia J ^c   Leitch, Andrew R ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b INSTITUTE OF BIOPHYSICS   (Czech Republic)

^c ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN; CYTOSINE; DNA DIRECTED RNA POLYMERASE; PLANT PROTEIN; PLANT RNA; RIBONUCLEASE III; SMALL INTERFERING RNA; SMALL UNTRANSLATED RNA;

ANGIOSPERM; ARABIDOPSIS; CHEMISTRY; CHROMATIN; CLASSIFICATION; DNA METHYLATION; ENZYMOLOGY; GENETIC EPIGENESIS; GENETICS; GYMNOSPERM; METABOLISM; METHYLATION; PHYLOGENY; PLANT GENE; PLANT GENOME;

ANGIOSPERMS; ARABIDOPSIS; CHROMATIN; CYTOSINE; DNA METHYLATION; DNA-DIRECTED RNA POLYMERASES; EPIGENESIS, GENETIC; GENES, PLANT; GENOME, PLANT; GYMNOSPERMS; METHYLATION; PHYLOGENY; PLANT PROTEINS; RIBONUCLEASE III; RNA, PLANT; RNA, SMALL INTERFERING; RNA, SMALL UNTRANSLATED;

EID: 84959288664     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv171     Document Type: Article

References (55)

1. Andika IB, et al. 2015. Differential contributions of plant Dicer-like proteins to antiviral defences against potato virus X in leaves and roots. Plant J. 81:781-793.
2. Becher H, et al. 2014. Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome. Plant J. 80:823-833.
3. Bennetzen JL, Wang H. 2014. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol. 65:505-530.
4. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-366.
5. Böhmdorfer G, et al. 2011. GMI1, a structural-maintenance-ofchromosomes- hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis. Plant J. 67:420-433.
6. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldó n T. 2009. Trim Al: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973.
7. Chang J-M, Di Tommaso P, Lefort V, Gascuel O, Notredame C. 2015. TCS: A web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic Acids Res. 43:W3-W6.
8. Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164-1165.
9. Dolgosheina EV, et al. 2008. Conifers have a unique small RNA silencing signature. RNA 14:1508-1515.
10. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Fei Q, Xia R, Meyers BC. 2013. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell 25:2400-2415.
12. Fischer S, et al. 2011. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics. Chapter 6:Unit 6.12.1-6.12.19.
13. Fuchs J, Jovtchev G, Schubert I. 2008. The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosom Res. 16:891-898.
14. Gao Z, et al. 2010. An RNA polymerase II- And AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465:106-109.
15. Grabherr MG, et al. 2011. Full-length transcriptome assembly from RNASeq data without a reference genome. Nat Biotechnol. 29:644-652.
16. Grover CE, Wendel JF. 2010. Recent insights into mechanisms of genome size change in plants. J Bot. 2010:1-8.
17. He XJ, Hsu YF, Pontes O, et al. 2009. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev. 23:318-330.
18. He XJ, Hsu YF, Zhu S, et al. 2009. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- And RNA-binding protein. Cell 137:498-508.
19. Hetzl J, Foerster AM, Raidl G, Mittelsten Scheid O. 2007. CyMATE: A new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. Plant J. 51:526-536.
20. Kelly LJ, et al. 2015. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytol: doi:10.1111/nph.13471.
21. Kenrick P, Crane PR. 1997. The origin and early evolution of plants on land. Nature 389:33-39.
22. Kovarik A, et al. 2005. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 169:931-944.
23. Kovach A, et al. 2010. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11:420.
24. Law J, et al. 2010. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol. 20:951-956.
25. Law J, et al. 2013. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498:385-389.
26. Leitch AR, Leitch IJ. 2012. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol. 194:629-646.
27. Leitch IJ, Leitch AR. 2013. Genome size diversity and evolution in land plants. In: Leitch IJ, Greilhuber J, Dolezel J, Wendel JF, editors. Plant genome diversity. Vol. 2. Vienna: Springer. p. 307-322.
28. Li FW, et al. 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A. 111:6672-6677.
29. Li L, Stoeckert CJ, Roos DS. 2003. Ortho MCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178- 2189.
30. Lim KY, et al. 2000. Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. Chromosoma 109:161-172.
31. Lisch D. 2013. How important are transposons in plant evolution? Nat Rev Genet. 14:49-61.
32. Liu Q, Feng Y, Zhu Z. 2009. Dicer-like (DCL) proteins in plants. Funct Integr Genomics. 9:277-286.
33. Margis R, et al. 2006. The evolution and diversification of Dicers in plants. FEBS Lett. 580:2442-2450.
34. Mathews S. 2009. Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. Am. J. Bot. 96:228-236.
35. Matzke MA, Kanno T, Matzke AJM. 2015. RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Annu Rev Plant Biol. 66:243-267.
36. Matzke MA, Mosher RA. 2014. RNA-directed DNA methylation: An epigenetic pathway of increasing complexity. Nat Rev Genet. 15:394-408.
37. Metcalfe CJ, Casane D. 2013. Accommodating the load: The transposable element content of very large genomes. Mob Genet Elements. 3:e24775.
38. Morse AM, et al. 2009. Evolution of genome size and complexity in Pinus. PLoS One 4:e4332.
39. Notredame C, Higgins DG, Heringa J. 2000. T-coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302:205-217.
40. Nuthikattu S, et al. 2013. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiol. 162:116-131.
41. Nystedt B, et al. 2013. The Norway spruce genome sequence and conifer genome evolution. Nature 497:579-584.
42. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA. 2010. Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery. BMC Genomics 11:180.
43. Ream TS, et al. 2009. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA Polymerase II. Mol Cell. 33:192-203.
44. Sasaki T, Lorković ZJ, Liang SC, Matzke AJM, Matzke MA. 2014. The ability to form homodimers is essential for RDM1 to function in RNA-directed DNA methylation. PLoS One 9:e88190.
45. Schauer SE, Jacobsen SE, Meinke DW, Ray A. 2002. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 7:487-491.
46. Song X, et al. 2012. Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J. 69:462-474.
47. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
48. Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE. 2013. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352-364.
49. Tucker SL, Reece J, Ream TS, Pikaard CS. 2010. Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization. Cold Spring Harb Symp Quant Biol. 75:285-297.
50. Wan L-C, et al. 2012. Identification and characterization of small noncoding RNAs from Chinese fir by high throughput sequencing. BMC Plant Biol. 12:146.
51. Wellman CH, Osterloff PL, Mohiuddin U. 2003. Fragments of the earliest land plants. Nature 425:282-285.
52. Woodhouse MR, Freeling M, Lisch D. 2006. Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors. PLoS Biol. 4:e339.
53. Zhang H, Ma ZY, et al. 2013. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A. 110:8290-8295.
54. Zhang J, Wu T, et al. 2013. Dynamic expression of small RNA populations in larch (Larix leptolepis). Planta 237:89-101.
55. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. 2004. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136:2621-2632.