ObjectiveTo screen and validate key enzyme genes affecting the polysaccharide content in different Polygonatum species and perform in-depth amino acid sequence analysis by transcriptomic analysis of P. zanlanscianense， P. kingianum， and P. cyrtonema rhizomes to enrich the transcriptome data of Polygonatum plants and provide references for polysaccharide biosynthesis mechanism and genetic improvement. MethodThe Polygonatum transcriptome was sequenced and analyzed using the Illumina NovaSeq high-throughput sequencing platform， and the differences in the transcriptomes of the three Polygonatum species were compared and according to the annotations of Nr， Gene Ontology （GO）， and Kyoto Encyclopedia of Genes and Genomes （KEGG） databases. The key enzymes in the polysaccharide metabolism pathway were screened， and the expression of key enzyme genes was clustered and correlated with the polysaccharide content. Finally， Real-time polymerase chain reaction （Real-time PCR） was performed to validate the eight key enzyme genes， and the key genes of polysaccharide biosynthesis were further screened for homologous gene sequence analysis in combination with sequencing results， followed by constructing phylogenetic trees， predicting motifs， conserved structural domains， protein sequence isoelectric points， and molecular weights， and constructing 3D protein structures by using homology modeling method. ResultThe annotation of the Nr database revealed that three Polygonatum species had the highest gene homology with Asparagus officinalis. GO database annotation results showed that three Polygonatum species differed significantly in binding， catalytic activity， metabolic processes， and cellular components， while the KEGG pathway annotation results indicated that three Polygonatum species differed significantly in the starch and sucrose metabolic pathway and galactose metabolic pathway. According to clustering analysis， correlation analysis， Real-time PCR， expression profiles， and structural and functional predictions of amino acid sequences， the key enzyme significantly affecting the polysaccharide content in different Polygonatum species was inferred to be β-fructofuranosidase （sacA）. ConclusionSacA may be the main influencing factor for the difference in polysaccharide content of Polygonatum， and is also an important reason why Polygonatum polysaccharides are mainly fructans.