小桐子YABBY全基因组家族成员的鉴定、表达和可变剪接分析

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

摘要:

为发掘能源植物小桐子（Jatropha curcas）的YABBY转录因子，以最新公布的小桐子基因组序列为参考，在全基因组层面鉴定出5个亚家族的7个YABBY基因，同一亚家族的成员具有相似的氨基酸序列、基因结构和保守基序组成。YAB2和FIL/YAB3亚家族的2个旁系同源基因对（JcYAB2A/JcYAB2B、JcYAB1/JcYAB3）具有良好的共线性关系，表明片段复制或全基因组复制是小桐子YABBY家族扩张的主要方式。纯化选择是进化的主要动力，而YAB2亚家族成员可能在进化中经历了更明显的功能分化。基因表达模式和蛋白互作预测分析表明JcYAB2B和JcYAB3可能在种子的发育过程中起到重要的调控作用；同时，细胞分裂素、干旱或高盐胁迫处理抑制了大多数JcYABs成员的基因表达。此外，转录组测序结合qRT-PCR分析表明，低温处理有效诱导JcYAB2A和JcYAB2B的基因表达模式发生变化，并伴随着新的、截短的可变剪接转录本的动态积累。因此，推测JcYABs可能通过剪接体的功能竞争或功能互补参与低温响应的调节，这些结果有助于更好地了解YABBY家族成员的功能分化并阐明可变剪接如何调控小桐子低温响应的分子机制。

关键词:小桐子;YABBY基因家族;可变剪接;生物信息学;基因表达

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