Abstract:

In order to explore the characteristics and function of PEBP gene family in Cymbidium faberi, the gene was cloned by reverse transcription-polymerase chain reaction (RT-PCR) combined with rapid-amplification of cDNA ends (RACE). R language, CodonW, CHIPS and CUSP software were used to analyze the codon preference, and the protein structure and function of the gene were predicted by using bioinformatics tools. The results showed that the cDNA sequence of PEBP gene contained 531 bp open reading frame (ORF) and encoded 176 amino acids. The gene was named as CfPEBP(Accession No. MT795710). The molecular formula of CfPEBP was C₈₈₂H₁₃₆₆N₂₅₄O₂₆₀S₅ with molecular weight of 19 848.39 u, pI of 6.42, and phosphorylation sites of 15. CfPEBP protein has no signal peptide domain and has PEBP functional domain. Phylogenetic tree analysis showed that CfPEBP protein had the closest evolutionary distance with FT gene of Cymbidium goeringii, and the homology was 100%. Codon preference analysis showed that the codon preference of CfPEBP was not obvious; based on the relative synonymous codon usage (RSCU) value, GGC, AGA, AGU, AAG, CCA, CUC (RSCU≥2) were the most preferred codons. The RSCU value analysis of PEBP gene in 18 species showed that there were more than 25 codons with RSCU value>1 in Cymbidium faberi, Oncidium hybrid(KJ909968), Oncidium hybrid(EU583502), Dendrobium hybrid(MF063061), Musa acuminata(KF853468) and Ipomoea nil(AB154823). PEBP family genes had more preference than other codons for GGC, AGG, AGA, AGC, AGU, UGC, GAG, AAG, UAC, GCC, CCA, CUC. The relative expression level of CfPEBP gene was the highest in the leaves of Cymbidium faberi at flowering stage, followed by flower bud at bud stage and inflorescence rachis at full-blossom stage. This study provided the basis for further study on the function of CfPEBP gene.

Key words: Cymbidium faberi, PEBP, bioinformatics analysis, codon usage bias, expression