Genome-wide identification and expression profiling of AP2/ERF superfamily genes under stress conditions in dark jute (Corchorus olitorius L.)

The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TF) in plants that play a vital role in regulating plant growth, development and stress response. A total of 119 CoAP2/ERF genes were identified from the dark jute genome, one of the most important bast fibre crops. Among these, 17 were AP2, 97 ERF, 4 RAV and 1 Soloist gene family. Phylogenetic analysis revealed that the AP2/ERF genes can be divided into 10 groups. These genes were distributed randomly across the linkage groups and found three tandem and eight segmental duplications which arose from ancient duplication events. Expression profiling of CoAP2/ERF genes was assessed using RNA-Seq data and qRT-PCR analysis in tissues during development and under biotic (Macrophomina phaseolina) and abiotic (waterlogging, salinity, drought) stresses. CoERF-21, CoERF-34 and CoERF-39 genes were significantly upregulated during waterlogging stress and CoDREB-11, CoDREB-14 and CoRAV-01 genes were upregulated under salinity and drought stress condition. Gene evolution analysis among the Malvaceae family showed dark jute were separated 14 and 22 Mya from cacao and cotton respectively and expression correlation analysis revealed the functions of superfamily genes were expanded and enhanced through gene duplication. These findings provide new insights into AP2/ERF gene evolution, divergence in dark jute and considered a valuable resource for further functional validation as well as for utilization in stress resistance variety development program.