The SAGA of pineapple: genome-wide identification and tissue-specific expression of Spt-Ada-Gcn5-acetyltransferase (SAGA) complex

Protein complexes involved in epigenetic regulation can recruit transcriptional machinery to control gene expression. The Spt-Ada-Gcn5-acetyltransferase (SAGA) is a chromatin-modifying transcriptional co-activator with an independent role in regulating gene transcription. We performed a genome-wide analysis to identify SAGA complex including phylogenetic analysis, chromosomal location, conserved protein domains, and gene expression analysis in pineapple. A total of 18 genes associated with SAGA complex were identified and divided into five distinct groups (ADAs, DUBm, SPTs, TAFs and other subunits) based on their relationships with orthologs in Arabidopsis and rice. The SAGA genes were widely but unevenly distributed in 10 chromosomes and exon–intron structure varied from 1 to 35 introns. The TAFs was enriched with Transcription initiation factor IID while ADAs and SPTs have sequence-specific protein domains. The cis-elements enriched in ADAs were CGTCA (MeJA-responsiveness), G-box (UV lights), and DUBm had HSE (heat-stress element). While all SPTs had TCA-motif and TAFs had ARE (anaerobic-response element). The AcSPT20 and AcSGF11 were down-regulated in fruit, while AcTRA1 was expressed in flowers and AcSUS1 in roots. The AcSPT7, AcSGF29, and AcTAF12 were expressed at all the stages of fruit development. While 3 TAFs and 7 other SAGA genes did not express in any tissue and at any fruit development stage, respectively. The tissue-specific regulation of SAGA genes revealed a differential expression and showed spatial gene expression during fruit developmental stages. The gene structural diversification, distinct motifs in SAGA subunits, and variation in gene expression indicates that the members of SAGA gene family might be functionally diverse.