title: Divergent evolution of the chloroplast small heat shock protein gene in the genera Rhododendron (Ericaceae) and Machilus (Lauraceae).
abstract: OBJECTIVE
  Evolutionary and ecological roles of the chloroplast small heat shock protein (CPsHSP) have been emphasized based on variations in protein contents; however, DNA sequence variations related to the evolutionary and ecological roles of this gene have not been investigated. In the present study, a basal angiosperm, Machilus, together with the eudicot Rhododendron were used to illustrate the evolutionary dynamics of gene divergence in CPsHSPs.
  
  
  METHODS
  Degenerate primers were used to amplify CPsHSP-related sequences from 16 Rhododendron and eight Machilus species that occur in Taiwan. Manual DNA sequence alignment was carried out according to the deduced amino acid sequence alignment performed by CLUSTAL X. A neighbour-joining tree was generated in MEGA using conceptual translated amino acid sequences from consensus sequences of cloned CPsHSP genes from eight Machilus and 16 Rhododendron species as well as amino acid sequences of CPsHSPs from five monocots and seven other eudicots acquired from GenBank. CPsHSP amino acid sequences of Funaria hygrometrica were used as the outgroups. The aligned DNA and amino acid sequences were used to estimate several parameters of sequence divergence using the MEGA program. Separate Bayesian inference of DNA sequences of Rhododendron and Machilus species was analysed and the resulting gene trees were used for detection of putative positively selected amino acid sites by the Codeml program implemented in the PAML package. Mean hydrophobicity profile analysis was performed with representative amino acid sequences for both Rhododendron and Machilus species by the Bioedit program. The computer program SplitTester was used to examine whether CPsHSPs of Rhododendron lineages and duplicate copies of the Machilus CPsHSPs have evolved functional divergence based on the hydrophobicity distance matrix.
  
  
  RESULTS
  Only one copy of the CPsHSP was found in Rhododendron. However, a higher evolutionary rate of amino acid substitutions in the Hymenanthes lineage of Rhododendron was inferred. Two positively selected amino acid sites may have resulted in higher hydrophobicity in the region of the alpha-crystallin domain (ACD) of the CPsHSP. By contrast, the basal angiosperm, Machilus, possessed duplicate copies of the CPsHSP, which also differed in their evolutionary rates of amino acid substitutions. However, no apparent relationship of ecological relevance toward the positively selected amino acid sites was found in Machilus.
  
  
  CONCLUSIONS
  Divergent evolution was found for both Rhododendron lineages and the paralogues of CPsHSP in Machilus that were directed to the shift in hydrophobicity in the ACD and/or methionine-rich region, which might have played important roles in molecular chaperone activity.
authors.affiliation: Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan.
authors.forename: Miao-Lun
authors.initials: ML
authors.lastname: Wu
authors.forename: Tsan-Piao
authors.initials: TP
authors.lastname: Lin
authors.forename: Min-Yi
authors.initials: MY
authors.lastname: Lin
authors.forename: Yu-Pin
authors.initials: YP
authors.lastname: Cheng
authors.forename: Shih-Ying
authors.initials: SY
authors.lastname: Hwang
mesh_terms: D000595:Amino Acid Sequence; D002736:Chloroplasts / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage; D014644:Genetic Variation; D050888:Heat-Shock Proteins, Small / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000502:physiology; D057927:Hydrophobic and Hydrophilic Interactions; D019770:Lauraceae / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D029793:Rhododendron / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D050888:Heat-Shock Proteins, Small