Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.
Guo
An-Yuan
AY
College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.
Zhu
Qi-Hui
QH
Gu
Xiaocheng
X
Ge
Song
S
Yang
Ji
J
Luo
Jingchu
J
D001665:Binding Sites; D017124:Conserved Sequence; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000032:analysis*; D005810:Multigene Family; D010802:Phylogeny; D014157:Transcription Factors; D016335:Zinc Fingers
D035683:MicroRNAs; D014157:Transcription Factors