Sequencing-by-synthesis – based Illumina sequencing platform can directly show the read length within 100 bp, in which the BMS-870145 relative abundance of specific RNA can be calculated according to the measured frequency of occurrence. This sequencing platform has been widely used in research fields such as functional genomics, cancer and other complex diseases, agricultural resources, and microbiology. In this study, the Illumina high-throughput sequencing technology and bioinformatics analysis were used to obtain the basic information on transcriptome and small RNAs in A. konjac and A. bulbifer. These dataset will serve as a public information platform for gene expression, genomics, and functional genomics in Amorphophallus. All-unigenes were aligned to the COG database to predict their possible functions. According to the Nr hits, a total of 21,610 sequences were assigned to 25 BMS-646786 categories in the COG database. The cluster of ����General function prediction���� was the largest group, followed by ����Transcription���� and ����Replication, recombination, and repair���� groups. Extracellular structures, nuclear structure, and RNA processing and modification were among the smallest categories. The gene ontology functional annotation can be obtained according to the Nr annotation information. GO comprises three ontologies that describe molecular functions, cellular components, and biological processes. A total of 27,773 transcripts of Amorphophallus were involved in various life activities. In a GO classification system, the three broad categories are molecular function, biological process, and cell components. Among them, 25,109 all-unigenes were involved in molecular functions, 40,810 all-unigenes were involved in biological processes, and 54,943 allunigenes were involved in cellular components. These broad categories are further divided into 44 small categories, in which the cells, cell parts, and organelles belonging to the cellular component category include the highest number of genes. Only a few all-unigenes were assigned to virion, cell killing, nitrogen utilization, and translation regulator activity. The target genes were predicted based on the characteristics of high complementarity of miRNAs with the target gene sequence. The results showed that 1197 transcripts of A. konjac were the potential target genes of miRNAs. Some target genes exhibited no definite functions, while the annotated targets are involved in transcriptional regulation, metabolism, signal transduction, stress response, electronic transmission, and other life processes.