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Backgrounds  Pomegranate is an excellent tree species with nutritional, medicinal, ornamental and ecological values. Studies have confirmed that SPL factors play an important role in floral transition and flower development.    Results  Used bioinformatics methods, 15 SPL (SQUAMOSA promoter-binding protein-like) genes were identified and analyzed from the ‘Taishanhong’ pomegranate ( P. granatum  L.) genome. Phylogenetic analysis showed that PgSPLs were divided into six subfamilies (G1 ~ G6). PgSPL promoter sequences contained multiple  cis -acting elements associated with abiotic stress or hormonal response. Based on the transcriptome data, expression profiles of different tissues and different developmental stages showed that  PgSPL  genes had distinct temporal and spatial expression characteristics. The expression analysis of miR156 in small RNA sequencing results showed that miR156 negatively regulated the expression of target genes. qRT-PCR analysis showed that the expression levels of  PgSPL2 ,  PgSPL3 ,  PgSPL6 ,  PgSPL11  and  PgSPL14  in leaves were significantly higher than those in buds and stems ( p  < 0.05). The expression levels of  PgSPL5 ,  PgSPL12  and  PgSPL13  in flower buds were significantly higher than that in leaves and stems ( p  < 0.05). The full-length of coding sequence of  PgSPL5  and  PgSPL13  were obtained by homologous cloning technology. The full length of  PgSPL5  is 1020 bp, and  PgSPL13  is 489 bp, which encodes 339 and 162 amino acids, respectively. Further investigation revealed that  PgSPL5  and  PgSPL13  proteins were located in the nucleus. Exogenous plant growth regulator induction experiments showed that  PgSPL5  was up-regulated in leaves and stems.  PgSPL13  was up-regulated in leaves and down-regulated in stems. When sprayed with 6-BA, IBA and PP333 respectively,  PgSPL5  and  PgSPL13  were up-regulated most significantly at P2 (bud vertical diameter was 5.1 ~ 12.0 mm) stage of bisexual and functional male flowers.    Conclusions  Our findings suggested that  PgSPL2 ,  PgSPL3 ,  PgSPL6 ,  PgSPL11  and  PgSPL14  played roles in leaves development of pomegranate.  PgSPL5 ,  PgSPL12  and  PgSPL13  played roles in pomegranate flower development.  PgSPL5  and  PgSPL13  were involved in the response process of different plant hormone signal transduction in pomegranate development. This study provided a robust basis for further functional analyses of  SPL  genes in pomegranate.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03171-7.

Genome-wide identification, gene cloning, subcellular location and expression analysis of SPL gene family in P. granatum L