PMID- 21388541
OWN - NLM
STAT- MEDLINE
DCOM- 20110614
LR  - 20211020
IS  - 1471-2148 (Electronic)
IS  - 1471-2148 (Linking)
VI  - 11
DP  - 2011 Mar 9
TI  - Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid 
      diversification in structure and function.
PG  - 63
LID - 10.1186/1471-2148-11-63 [doi]
AB  - BACKGROUND: Plants contain numerous Su(var)3-9 homologues (SUVH) and related 
      (SUVR) genes, some of which await functional characterization. Although there 
      have been studies on the evolution of plant Su(var)3-9 SET genes, a systematic 
      evolutionary study including major land plant groups has not been reported. 
      Large-scale phylogenetic and evolutionary analyses can help to elucidate the 
      underlying molecular mechanisms and contribute to improve genome annotation. 
      RESULTS: Putative orthologs of plant Su(var)3-9 SET protein sequences were 
      retrieved from major representatives of land plants. A novel clustering that 
      included most members analyzed, henceforth referred to as core Su(var)3-9 
      homologues and related (cSUVHR) gene clade, was identified as well as all 
      orthologous groups previously identified. Our analysis showed that plant 
      Su(var)3-9 SET proteins possessed a variety of domain organizations, and can be 
      classified into five types and ten subtypes. Plant Su(var)3-9 SET genes also 
      exhibit a wide range of gene structures among different paralogs within a family, 
      even in the regions encoding conserved PreSET and SET domains. We also found that 
      the majority of SUVH members were intronless and formed three subclades within 
      the SUVH clade. CONCLUSIONS: A detailed phylogenetic analysis of the plant 
      Su(var)3-9 SET genes was performed. A novel deep phylogenetic relationship 
      including most plant Su(var)3-9 SET genes was identified. Additional domains such 
      as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial 
      PreSET/SET/PostSET domain organization. At least three classes of gene structures 
      had been formed before the divergence of Physcomitrella patens (moss) from other 
      land plants. One or multiple retroposition events might have occurred among SUVH 
      genes with the donor genes leading to the V-2 orthologous group. The structural 
      differences among evolutionary groups of plant Su(var)3-9 SET genes with 
      different functions were described, contributing to the design of further 
      experimental studies.
FAU - Zhu, Xinyu
AU  - Zhu X
AD  - State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, 
      Chinese Academy of Sciences, Beijing 100093, China.
FAU - Ma, Hong
AU  - Ma H
FAU - Chen, Zhiduan
AU  - Chen Z
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110309
PL  - England
TA  - BMC Evol Biol
JT  - BMC evolutionary biology
JID - 100966975
RN  - EC 2.1.1.- (Methyltransferases)
RN  - EC 2.1.1.- (SU(VAR)3-9)
SB  - IM
MH  - *Evolution, Molecular
MH  - Genes, Plant
MH  - Methyltransferases/*genetics
MH  - *Phylogeny
MH  - Plants/enzymology/*genetics
MH  - Sequence Alignment
MH  - Sequence Analysis, DNA
PMC - PMC3063831
EDAT- 2011/03/11 06:00
MHDA- 2011/06/15 06:00
PMCR- 2011/03/09
CRDT- 2011/03/11 06:00
PHST- 2010/07/30 00:00 [received]
PHST- 2011/03/09 00:00 [accepted]
PHST- 2011/03/11 06:00 [entrez]
PHST- 2011/03/11 06:00 [pubmed]
PHST- 2011/06/15 06:00 [medline]
PHST- 2011/03/09 00:00 [pmc-release]
AID - 1471-2148-11-63 [pii]
AID - 10.1186/1471-2148-11-63 [doi]
PST - epublish
SO  - BMC Evol Biol. 2011 Mar 9;11:63. doi: 10.1186/1471-2148-11-63.