Integrated mRNA and miRNA transcriptome analysis on the regulational of mechanism tuber expansion in Yam

Abstract

Background Tuber is the storage organ of yam derived from modified stems. The development of tube expansion is a complex process and depends on the expression of genes that are involved by environmental and endogenous factors. However, little is known about the mechanism that regulates tuber expansion. In this study, in order to identify genes and miRNAs involvd in tuber enlargement, we examined the transcriptomes and small RNA in tuber initiation and expansion stages. Results A total of 14238 transcripts expressed differentially in the expansion stage were firstly identified using transcriptome technology. Of these, 5723 and 8515 genes were up and down regulated, respectively. The functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis and signalling transduction pathways at the transcriptional level, suggesting these DEGs are somehow involved in the responses of tuber expansion. In additional, 536 transcription factor genes were found differently expression in expansion stage at the transcript level. REVEILLE 6-like is identified to be up regulated in circadian rhythm pathway. REVEILLE 6-like LHY protein, zinc finger CCCH domain-containing protein 14, and DELLA genes were involved up regulated in expansion stage. Moreover, these genes were respectively involved in circadian rhythm pathway, starch and sucrose metabolism pathway, and GA pathway by KEGG analysis. Noteworthy, the analysis of the data showed that there were 23 known tuber miRNAs belonged to 11 miRNA families, and 50 novel miRNAs, miRNA160 miRNA396, and miR535 may be involved in complexity network to regulate cell division and differentiation in the expansion stage in yam. The integrated analysis of miRNA-mRNA were identified to be preferentially expressed in hormone signalling in expansion stage, like the ARFs by miRNA160 highlighting the involvement of miRNA-mRNA in the regulation hormone of tuber expansion in yam. Conclusion The transcriptome and miRNA datasets presented here identified a subset of candidate genes and miRNAs putatively associated with tuber expansion in yam, thus a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.