De Novo Gene Set Assembly of the Transcriptome of the Diploid, Oilseed-Crop Species Perilla Citriodora

High-quality gene sets are necessary for functional research of genes. Although the Perilla is commonly cultivated as an oil crop and a vegetable crop in Southeast Asia, the quality of its available gene set is insufficient. To construct a high-quality Perilla gene set, we sequenced the mRNA extracted from different tissues of Perilla citriodora, the wild species (2n = 20) of Perilla. To make a high-quality gene set for P. citriodora, we compared the quality of assemblies produced by two well-known assemblers, Velvet and Trinity, and improved the de novo assembly pipeline by optimizing the k-mers and removing redundant sequences. We then selected representative transcripts for loci according to several criteria. The improved assembly yielded 86,396 total transcripts and 38,413 representative transcripts. We evaluated assembled transcripts by comparing them to 638 homologous Arabidopsis genes involved in fatty acid and TAG biosynthesis pathways. The high proportions of full-length genes and transcripts matching known genes in other species among the assembled transcripts indicate that the P. citriodora gene set can be applied in future functional studies. Our study provides a reference P. citriodora gene for further studies and a valuable genetic resource to elucidate the molecular basis of various metabolisms.