Genome-wide Characterization, Expression Profiles and Alternative Splicing Events of YABBY Family Genes in Jatropha curcas

Abstract:

In order to explore the YABBY transcription factor of Jatropha curcas, seven YABBY genes from five subfamilies were identified at the genome-wide level based on the newly published genome sequence of J. curcas. Members of the same subfamily had similar amino acid sequence, gene structure and conserved motifs. Two pairs of paralogs from YAB2 (JcYAB2A/JcYAB2B) and FIL/YAB3 (JcYAB1/JcYAB3) subfamily showed good collinearity, indicating that segmental duplication/whole genome duplication was the primary cause of YABBY gene family expansion. Purifying selection might be the main impetus during evolution, while candidates of YAB2 subgroup underwent more significant functional divergence. The expression patterns together with protein-protein interaction prediction suggested that JcYAB2B and JcYAB3 might play crucial roles in seed development, meanwhile the transcription of most JcYABs were remarkably repressed under exogenous cytokinin, drought or salinity stress. In addition, RNA sequencing and qRT-PCR analysis confirmed that the paralogous gene pair JcYAB2A/JcYAB2B exhibited differential cold-responsive transcription in leaves, and their newly identified transcripts were both dynamically accumulated during cold treatment. Therefore, it was speculated that JcYABs might participate in the regulation of low temperature response through functional competition or functional complementarity of spliceosome. These would help to understand the evolution of YABBY family, and elucidate how AS events play a crucial regulatory role in cold response of J. curcas.

Key words:Jatropha curcas;YABBY family gene;Alternative splicing;Bioinformatics;Gene expression