title: Evolution and divergence of SBP-box genes in land plants.
abstract: BACKGROUND
  Squamosa promoter binding protein (SBP)-box family genes encode plant-specific transcription factors that control many important biological functions, including phase transition, inflorescence branching, fruit ripening, and copper homeostasis. Nevertheless, the evolutionary patterns of SBP-box genes and evolutionary forces driving them are still not well understood.
  
  
  METHODS
  104 SBP-box gene candidates of five representative land plants were obtained from Phytozome database (v10.3). Phylogenetic combined with gene structure analyses were used to identify SBP-box gene lineages in land plants. Gene copy number and the sequence and structure features were then compared among these different SBP-box lineages. Selection analysis, relative rate tests and expression divergence were finally used to interpret the evolutionary relationships and divergence of SBP-box genes in land plants.
  
  
  RESULTS
  We investigated 104 SBP-box genes from moss, Arabidopsis, poplar, rice, and maize. These genes are divided into group I and II, and the latter is further divided into two subgroups (subgroup II-1 and II-2) based on phylogenetic analysis. Interestingly, subgroup II-1 genes have similar sequence and structural features to group I genes, whereas subgroup II-2 genes exhibit intrinsic differences on these features, including high copy numbers and the presence of miR156/miR529 regulation. Further analyses indicate that subgroup II-1 genes are constrained by stronger purifying selection and evolve at a lower substitution rate than II-2 genes, just as group I genes do when compared to II genes. Among subgroup II-2 genes, miR156 targets evolve more rapidly than miR529 targets and experience comparatively relaxed purifying selection. These results suggest that group I and subgroup II-1 genes under strong selective constraint are conserved. By contrast, subgroup II-2 genes evolve under relaxed purifying selection and have diversified through gene copy duplications and changes in miR156/529 regulation, which might contribute to morphological diversifications of land plants.
  
  
  CONCLUSIONS
  Our results indicate that different evolutionary rates and selection strengths lead to differing evolutionary patterns in SBP-box genes in land plants, providing a guide for future functional diversity analyses of these genes.
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany of the Chinese Academy of Sciences, Kunming, 650201, China. sdchang@mail.kib.ac.cn.
authors.forename: Shu-Dong
authors.initials: SD
authors.lastname: Zhang
authors.affiliation: BGI-Yunnan, BGI-Shenzhen, Kunming, 650106, China. linglizhen@genomics.cn.
authors.forename: Li-Zhen
authors.initials: LZ
authors.lastname: Ling
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany of the Chinese Academy of Sciences, Kunming, 650201, China. tingshuangyi@mail.kib.ac.cn.
authors.forename: Ting-Shuang
authors.initials: TS
authors.lastname: Yi
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics; D044002:Bryophyta / Q000235:genetics; D019669:Embryophyta / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005810:Multigene Family / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D032107:Populus / Q000235:genetics; D003313:Zea mays / Q000235:genetics
chemical_list: D010940:Plant Proteins; C402744:SBP protein, Papaver rhoeas