Abstract
The leaf and the flower are vital plant organs owing to their roles in photosynthesis and reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and transcription factors (TFs) are very important to the development of these organs. Liriodendron chinense is a common ornamental tree species in southern China with an unusual leaf shape and tulip-like flowers. The genetic mechanisms underlying leaf and flower development in L. chinense and the miRNA-lncRNA-TF regulatory networks are poorly studied. Through the integration and analysis of different types of sequencing data, we identified the miRNA-lncRNA-TF regulatory networks that were related to leaf and flower development. These networks contained 105 miRNAs, 258 lncRNAs, 393 TFs, and 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 and lch-lnc7374-miR156j-SPL9 were potential regulators of stamen and pistil development in L. chinense, respectively. miRNA-lncRNA-mRNA regulatory networks were shown to impact anther development, male and female fertility, and petal color by regulating the biosynthesis of phenylpropanoid metabolites. Phenylpropanoid metabolite biosynthesis genes and TFs that were targeted by miRNAs and lncRNAs were differentially expressed in the leaf and flower. Moreover, RT-qPCR analysis confirmed 22 differentially expressed miRNAs, among which most of them showed obvious leaf or flower specificity; miR157a-SPL and miR160a-ARF module were verified by using RLM-RACE, and these two modules were related to leaf and flower development. These findings provide insight into the roles of miRNA-lncRNA-mRNA regulatory networks in organ development and function in L. chinense, and will facilitate further investigation into the regulatory mechanisms of leaf and flower development in L. chinense.
Highlights
The development of the leaf and the flower is an important part of plant growth
To allow full interpretation of the phenylpropanoid biosynthesis pathway, we integrated data from all differentially expressed genes (DEGs) involved in the phenylpropanoid biosynthesis pathway, and identified 14 gene families that participated in phenylpropanoid biosynthesis: phenylalanine ammonia lyase (PAL), 4-coumarateCoA ligase (4CL), cinnamate 4-hydroxylase (C4H), cinnamoyl-CoA reductase (CCR), ferulate 5-hydroxylase (F5H), caffeic acid O-methyltransferase (COMT), caffeoyl-CoA O-methyltransferase (CCoAOMT), hydroxyl cinnamoyl transferase (HCT), cinnamyl alcohol dehydrogenase (CAD), POD, coumarate 3 hydroxylase (C3H), coniferyl-aldehyde dehydrogenase (CALDH), beta-glucosidase (β-G), and coniferyl-alcohol glucosyltransferase (CGT) (Figure 2A)
We found that Long non-coding RNAs (lncRNAs)-targeted MYB transcription factors (TFs) were involved in the regulation of flower development, and in the regulation of phenylpropanoid biosynthesis (Figure 8). lncRNA-MYB regulatory patterns, such as lchlnc0003-MYB4, lch-lnc5422-MYB5, lch-lnc6438-MYB39, lchlnc6439-MYB44, and lch-lnc6440-MYB340 may be related to the biosynthesis of flavonoids and anthocyanins, because previous studies have revealed that MYB4, MYB5, MYB39, MYB44, and MYB340 participate in the regulation of flavonoids and anthocyanins biosynthesis (Moyano et al, 1996; Liu et al, 2013; Sun et al, 2016; Wang et al, 2020; Wei et al, 2020)
Summary
The development of the leaf and the flower is an important part of plant growth. The leaf is a lateral organ, with a complex and sequential development process comprising leaf primordium initiation (initiated from the lateral of shoot apical meristem), leaf polarity establishment, development phase transition, leaf morphology modulation, and leaf senescence (Yang et al, 2018). CUPSHAPED COTYLEDON (CUC), GROWTH REGULATING FACTOR (GRF), TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP), and HOMEDOMAIN-LEUCINE ZIPPER (HD-ZIP) are TFs related to leaf development that determine leaf serration formation, control leaf size and longevity, and regulate leaf polarity establishment (Hasson et al, 2011; Bou-Torrent et al, 2012; Debernardi et al, 2014; Bresso et al, 2018). These TFs regulate leaf and flower development by activating or repressing the activities of their downstream genes. The activities of TFs and their downstream genes are regulated by miRNAs and lncRNAs
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