Article thumbnail

Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function

By Xinyu Zhu, Hong Ma and Zhiduan Chen
Topics: Research Article
Publisher: BioMed Central
OAI identifier:
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles


  1. (1998). A combined analysis of genomic and primary protein structure defines the phylogenetic relationship of new members if the T-box family. Genomics
  2. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution
  3. (2006). A: Pfam: clans, web tools and services.
  4. (2006). Aalen RB: The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9. Nucleic Acids Research
  5. (2001). Aalen RB: The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Research
  6. (2001). Allis CD: Translating the histone code. Science
  7. (2005). Analysis of evolution of exon-intron structure of eukaryotic genes. Briefings in Bioinformatics
  8. (2002). Aravind L: The role of lineage-specific gene family expansion in the evolution of eukaryotes.
  9. (2006). Avramova Z: Origin of the Bacterial SET Domain Genes: Vertical or Horizontal? Molecular Biology and Evolution
  10. (2000). Conery JS: The evolutionary fate and consequences of duplicate genes. Science
  11. (2004). Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
  12. (2006). CR: Intron gain and loss in segmentally duplicated genes in rice. Genome Biology
  13. (2001). Croteau RB: Genomic organization of plant terpene synthases and molecular evolutionary implications. Genetics
  14. (2007). dePamphilis CW: Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth.
  15. (1997). DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research
  16. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach.
  17. (2003). Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology
  18. (2008). Gene structure dynamics and divergence of the polygalacturonase gene family of plants and fungus. Genome
  19. (2005). Girke T: Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiology
  20. (2005). H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Molecular and Cellular Biology
  21. (2006). Heterochromatin proteins and the control of heterochromatic gene silencing in Arabidopsis.
  22. (2006). High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell
  23. (2004). Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Molecular Biology and Evolution
  24. (2003). I: Histone modifications in Arabidopsis- high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin.
  25. (2000). Kado CI: The origin of prokaryotic C2H2 zinc finger regulators. Trends in Microbiology
  26. (2003). Kaeppler SM: Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiology
  27. (2001). Lecharny A: Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila. Genome Research
  28. (2000). Li W: Fundamentals of Molecular Evolution.
  29. (2006). Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell
  30. (1993). Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution
  31. (1990). MS: The AT-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure.
  32. (2004). Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics
  33. (2001). Nekrutenko A: Evolutionary analyses of the human genome. Nature
  34. (2001). NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth.
  35. (1951). On Information and Sufficiency.
  36. (1993). Organization, inducibleexpression and chromosome localization of the human HMG-I(Y) nonhistone protein gene.
  37. (2001). Ostell JM: Spidey: a tool for mRNA-to-genomic alignments. Genome Research
  38. (2006). P: PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
  39. (2006). P: SMART 5: domains in the context of genomes and networks.
  40. (2000). Pabo CO: DNA recognition by Cys2His2 zinc finger proteins. Annual Review of Biophysics and Biomolecular Structure
  41. (1994). Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene.
  42. (1995). PJ: The Drosophila trithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins. Mechanisms of Development
  43. (2006). Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome.
  44. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics
  45. (2005). Reuter G: Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis.
  46. (1999). RL: Rubisco small and large subunit N-methyltransferases. Bi- and mono-functional methyltransferases that methylate the small and large subunits of Rubisco.
  47. (1993). Saumweber H: The enhancer of position-effect variegation of Drosophila, E(var)3-93D, codes for a chromatin protein containing a conserved domain common to several transcriptional regulators.
  48. (2004). SE: Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma
  49. (2002). Systematic identification of novel protein domain families associated with nuclear functions. Genome Research
  50. (2007). TC: Plant SET domain-containing proteins: structure, function and regulation. Biochimica et Biophysica Acta
  51. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution
  52. (1994). The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes.
  53. (2005). The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
  54. (1995). WD: High-level tuber expression and sucrose inducibility of a potato Sus4 sucrose synthase gene require 5’ and 3’ flanking sequences and the leader intron. Plant Cell
  55. (1993). WM: The Drosophila Polycomb-group gene Enhancer of zeste contains a region with sequence similarity to trithorax. Molecular and Cellular Biology