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 miRNAmediated 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 coexpressed 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.

Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations

“…In previous studies, 11 homeotic MADS-box genes, one AP2 gene and 31 methylation region-associated genes involved in stamen petaloid in lotus have been identified (Lin et al, 2018(Lin et al, , 2019. Moreover, miR172, as a negative regulator, was also important during the crucial early stages of stamen development in lotus (Zhang Y. et al, 2020). However, the 16 candidate genes responsible for stamen petaloid variations in our study do not belong to the MADS-box family.…”

“…A total of 54 genes located in 14 LD blocks that have known regulatory functions in the synthesis and transport of some proteins, cellular structure and jasmonate synthesis might be involved in the control of plant size in the development of lotus (Supplementary Figure S3J; Supplementary Table S4). CLE26 (Nn4g22977), ALA3 (Nn4g22982) and VEL1 (Nn8g40603) were significantly associated with plant size variations involved in the regulation of cell differentiation in the phloem of roots and stems during auxin polar transport, vesicle-mediated transportation and the transition of the meristem from vegetative to reproductive phases (Supplementary Table S4; Kim and Sung, 2010;Czyzewicz and De Smet, 2016;Zhang X. et al, 2020). The CLE26, ALA3 and VEL1 genes were expressed primarily in the root apical meristem, immature stamen and root, respectively (Supplementary Figure S5G).…”

“…Generally, the types of lotus flowers vary from few-petalled flowers to various double-petalled flowers because flowers with stamen petaloid and carpel petaloid fail to form normal floral patterns. These processes have been predicted to be influenced by several hormone-related candidate genes and transcription factors (TFs; Lin et al, 2018), and epigenetic regulation (methylation and miR172 family; Lin et al, 2019;Zhang Y. et al, 2020). The chromosomal-level genome assembly of lotus cv.…”

Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes

“…1 F, Table S3 ). Because our previous studies suggested that transposable elements (TEs) are an important source to give birth to novel miRNAs, particularly 24 nt miRNAs [ 34 ], the difference in TE activities between five wild lotuses might be associated with these novel 24nt miRNAs. There were 437, 343, 270, 210, and 186 circRNAs found in rhizomes from China, India, Russia, Australia, and Thailand lotus, while 52 high-quality circRNAs were detected in all five samples ( Fig.…”

Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield

“…Several studies have indicated that most of the essential miRNAs for biological processes target TFs or stress-response factors. In the absence of miRNAs and their regulation, plants would suffer developmental deficiencies in many critical developmental stages [ 73 , 74 ].…”