Transcriptome and small RNAome facilitate to study schaftoside in Desmodium styracifolium Merr

Abstract The traditional Chinese medicinal plant Desmodium styracifolium Merr. have efficient effect on preventing urinary calculi due to schaftoside. However, the schaftoside biosynthesis remains unknown. In this study, RNAseq transcriptomes and small RNAomes of leaves and flowers were sequenced and analyzed. There are 9955 differentially expressed genes DEGs and 86 differentially expressed microRNA miRNA identified. Pathway enrichment analysis show that phenylpropanoid biosynthesis and phenylalanine metabolism are over-represented in leaves when compared to flowers. A total of 30,934 simple sequence repeat SSR, 17,574 insertion-deletions InDels, and 86,882 single nucleotide polymorphisms SNPs were identified as gene-based markers. Schaftoside biosynthetic genes C-glucosyltransferase CGT and flavone synthase II FNSII and 1484 unigenes coexpressing with CGT and FNSII were predicted. Among them, 1038 unigenes containing gene-based marker coexpressed with CGT and 419 CGT-coexpressing unigenes can be successfully designed SSR markers. Moreover, 107 of 419 CGT-coexpressing unigenes containing SSR were randomly selected to validate the efficiency of SSR primers, which resulting 104 97.2 %) primers successfully amplified the polymerase chain reaction product and 54 (50.5 % primers are polymorphism primers. These results suggested that 211 polymorphic SSR markers could be further used for marker-assisted breeding MAB. Meanwhile, 6436 of 9955 DEGs containing gene-based marker differentially expressed in leaves when compared to flowers. Furthermore, 26 and 184 miRNA-targeted unigenes containing gene-based markers are CGT-coexpressing genes and DEGs, respectively. Candidate genes and gene-based markers identified in this study are useful resource, which lay a solid foundation for studying schaftoside biosynthesis, MAB, genetic map and comparative genomic study of D. styracifolium.