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Heat shock transcription factor (Hsf) plays a transcriptional regulatory role in plants during heat stress and other abiotic stresses. 31 non-redundant  ZmHsf  genes from maize were identified and clustered in the reference genome sequenced by Single Molecule Real Time (SMRT). The amino acid length, chromosome location, and presence of functional domains and motifs of all  ZmHsfs  sequences were analyzed and determined. Phylogenetics and collinearity analyses reveal gene duplication events in Hsf family and collinearity blocks shared by maize, rice and sorghum. The results of RNA-Seq analysis of anthesis and post-anthesis periods in maize show different expression patterns of  ZmHsf  family members. Specially,  ZmHsf26  of A2 subclass and  ZmHsf23  of  A6  subclass were distinctly up-regulated after heat shock (HS) at post-anthesis stage. Nanopore transcriptome sequencing of maize seedlings showed that alternative splicing (AS) events occur in  ZmHsf04  and  ZmHsf17  which belong to subclass A2 after heat shock. Through sequence alignment, semi-quantitative and quantitative RT-PCR, we found that intron retention events occur in response to heat shock, and newly splice isoforms,  ZmHsf04-II  and  ZmHsf17-II , were transcribed. Both new isoforms contain several premature termination codons in their introns which may lead to early termination of translation. The  ZmHsf04  expression was highly increased than that of  ZmHsf17 , and the up-regulation of  ZmHsf04-I  transcription level were significantly higher than that of  ZmHsf04-II  after HS.

Genome-wide identification, transcriptome analysis and alternative splicing events of Hsf family genes in maize