Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid (CGA) biosynthesis in leafy sweet potato

Abstract

Background Phenolic compounds play key roles in health protection and leafy sweet potato is an excellent source of total phenolics (TP). The chlorogenic acid (CGA) family, which includes caffeoylquinic acid (CQA), 3,4-O-dicaffeoylquinic acid (3,4-diCQA), 3,5-O-dicaffeoylquinic acid (3,5-diCQA) and 4,5-O-dicaffeoylquinic acid (4,5-diCQA), constitutes the major components of phenolic compounds in leafy sweet potato. However, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. The objective of present study is to dissect the mechanisms of CGA biosynthesis by using transcriptome, small RNA and degradome sequencing.Results Transcriptome sequencing of twelve samples (three replicates) from one low-CGA content genotype and one high-CGA content genotype at two stages (65 and 85 days after planting) identified a total of 2333 common differentially expressed genes (DEGs). The enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. In this study, functional genes CCR , CCoAOMT and HCT in the CGA biosynthetic pathway were uniformly downregulated, indicating the way to lignin was altered. Small RNA sequencing of the samples resulted in the identification of 171 microRNAs (miRNAs), including 149 known and 22 novel miRNAs. A total of 38 miRNAs were differentially expressed. Using in silico approaches, 1799 targets were predicated for 38 DE miRNAs. The target genes were enriched in lignin and phenylpropanoid catabolic process. Transcription factors (TFs) such as APETALA2/ethylene response factor ( AP2/ERF ) and Squamosa promoter binding protein -like ( SPL ) predicated in silico were validated in degradome sequencing. The association analysis of DE miRNAs and transcriptome datasets identified that MIR156 family targeted DHQ / SDH (3-dehydroquinate dehydratase/shikimate dehydrogenase), the key gene in the phenylpropanoid pathway , the result of which was validated by qRT-PCR. The expression trends of genes and miRNAs of qRT-PCR were consistent with the RNA and small RNA sequencing results.Conclusions This study established comprehensive functional genomic resources for the CGA biosynthesis and provided insights into the molecular mechanisms involving in this process. The results also enabled the first insights into the regulatory roles of mRNAs and miRNAs and offered candidate genes for leafy sweet potato improvement.