Genome-wide identification, characterization and functional prediction of the SPL gene family in sesame (Sesamum indicum L.)

Abstract

Abstract‘SQUAMOSA promoter binding protein-like’ (SPL) proteins are the plant-specific transcription factors (TFs) family, comprising a highly conserved SBP domain with two zinc-fingers. It plays a vital role in plant growth and development and stress responses in plants. The SPL TF family is well characterized in several plant species, nevertheless not yet accomplished in sesame (Sesamum indicum L.). In this study, we performed in silico identification, molecular characterization, phylogenetic relationship, cis-acting regulatory elements, protein-protein interaction, syntenic relationship, duplication events and RNA-seq based expression of sesame SPL genes. We identified a total 19 of SiSPL genes on 12 different LGs of sesame genome through comparing with the other plant species. The SiSPL genes varied in gene structures like 2–11 exons and 1–10 introns. The SiSPL proteins contained a highly conserved ‘SQUAMOSA-promoter binding protein’ (SBP, pfam03110), only found in plants. Further, SiSPL4 and SiSPL9 contained one extra domain called ‘Ank_2’ (pfam12796). The SiSPL genes were grouped into seven groups via phylogenetic analysis which showed the relationship with other plant species. Total 454 stress responsive ‘cis-regulatory’ elements were detected in the promoter region of 19 SiSPL genes indicating their possible involvement in stress responses. Furthermore, the available sesame transcriptomic data indicated that SiSPL genes varied in transcript accumulation between stressed vs. control samples. In particular, SiSPL9 (SIN_1016140), SiSPL12 (SIN_1017992) and SiSPL3 (SIN_1006254) might be drought responsive. Likewise, SiSPL8 (SIN_1013914), SiSPL15 (SIN_1023563) and SiSPL17 (SIN_1026466) was up-regulated in salinity conditions. Besides, the transcript abundance of SiSPL1 and SiSPL9 genes was higher in waterlogging conditions as compared to the control. To best of our knowledge, this is the first report of SPL gene family in sesame. The findings of this study will encourage further research into gene expression as well as functional analysis of SiSPL genes in sesame and other plant species.