Global identification of long non-coding RNAs involved in the induction of spinach flowering

Abstract

Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa

“…Samples from 5 different seedlings were pooled together as one biological sample. Three biological replicates from each genotype were used for RNA extraction and the Real-Time PCR (qPCR) analysis according to the previous research [ 11 , 131 , 132 ]. In brief, total RNAs were extracted by the DENAzist column RNA isolation kit.…”

“…What is still slightly ambiguous, is the putative roles of non-coding genes. Transcripts of non-coding genes have revealed regulatory functions in different pathways affecting flowering and the reproductive switch [ 11 ]. One of these types of transcripts is the long non-coding RNA known as lncRNA.…”

“…They are similar to coding mRNA in being transcribed by RNA Pol II and acquiring a poly-adenylated tail [ 12 ]; however, they are not translated into proteins. LncRNAs originate from intergenic regions or the intronic and exonic regions of the coding genes [ 11 ], and they usually regulate the expression of other genes and act as miRNA sequesters to allow the expression of mRNAs targeted by miRNA.…”

“…Similarly, several publications have identified lncRNAs implicated in bolting. Ghorbani et al [ 11 ] performed transcriptome and qPCR analyses to reveal lncRNAs and hub genes associated with spinach bolting in two accessions. Correspondingly, Tu et al [ 21 ] identified the miRNA-lncRNA-TF regulatory networks attributed to leaf and flower development in Liriodendron chinense , a common ornamental tree species in southern China.…”

Why lncRNAs were not conserved? Is it for adaptation?

“…In recent years, reports on the plant lncRNAs have demonstrated they act as key regulatory elements in nearly all developmental process, including root organogenesis (Ganguly et al, 2021), flowering time (Heo and Sung 2011;Ghorbani et al, 2021), photo morphogenesis (Wang et al, 2014), and reproduction (Zhang et al, 2014;Fang et al, 2019). The studies reported plant lncRNAs with diverse biological mechanisms played in developmental process, biotic and abiotic stress responses (Swiezewski et al, 2009;Heo and Sung, 2011;Wang et al, 2014).…”