Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Abstract

Background: Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant.Results: Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes.Conclusions: Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.

Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

“…Likewise, the chromatin remodeler ZmCHB101 affects the AS contexts in maize by altering the chromatin and histone modification status, as well as the elongation rate of RNA polymerase II in response to osmotic stress [ 28 ]. Moreover, noncoding RNAs have also emerged as key regulators of AS patterns in plants, which, in turn, influence the miRNA-mediated regulation of gene expression associated with different biological processes [ 29 , 30 , 31 , 32 , 33 , 34 ]. Together, these findings reveal an additional epigenetic layer in regulating AS in plants.…”

Multi-omics Analysis Reveals Whether and how Naphthylacetic Acid Affects the Quality of Rehmannia Glutinosa

“…Among them, only novel_miR_57 was upregulated, while novel_miR_65 and novel_miR_23 were downregulated in NT. 18nt miRNAs were also discovered in other plants [34]. These miRNAs enlarged its known miRNA database and their categories.…”

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

“…Since the first draft genome assembly of the lotus variety China Antique was released 9 , many genomic studies have been carried out on lotus, such as whole-genome resequencing 7 , 10 , 11 , transcriptomic 12 – 14 , miRNA-based 15 – 17 and gene family studies 18 , 19 . The recent chromosome-level assembly of the China Antique genome facilitates genome-wide studies of functional genes and the evolution of lotus, but a web-based public database of lotus is still unavailable 8 .…”

“…A total of 28,676 genes were defined as high-confidence genes, with 14,991, 20,878, 15,276, 5,924, 29,095, 20,325, and 28,310 annotated genes in the KOG, PFAM, GO, KEGG, Nr, SwissProt and TrEMBL databases, respectively ( Table 1 ) . The NGD also houses the sequences of 150,589 unique transcript isoforms based on RNA-seq and PacBio SMRT methods from our previous studies 14 , 17 . It also contains the sequences of 1,517 lotus transcription factors (TFs), which are classified into 56 TF (sub)families.…”