Differentially Expressed microRNAs and Target Genes Associated with Plastic Internode Elongation in Alternanthera philoxeroides in Contrasting Hydrological Habitats

Abstract

Phenotypic plasticity is crucial for plants to survive in changing environments. Discovering microRNAs, identifying their targets and further inferring microRNA functions in mediating plastic developmental responses to environmental changes have been a critical strategy for understanding the underlying molecular mechanisms of phenotypic plasticity. In this study, the dynamic expression patterns of microRNAs under contrasting hydrological habitats in the amphibious species Alternanthera philoxeroides were identified by time course expression profiling using high-throughput sequencing technology. A total of 128 known and 18 novel microRNAs were found to be differentially expressed under contrasting hydrological habitats. The microRNA:mRNA pairs potentially associated with plastic internode elongation were identified by integrative analysis of microRNA and mRNA expression profiles, and were validated by qRT-PCR and 5′ RLM-RACE. The results showed that both the universal microRNAs conserved across different plants and the unique microRNAs novelly identified in A. philoxeroides were involved in the responses to varied water regimes. The results also showed that most of the differentially expressed microRNAs were transiently up-/down-regulated at certain time points during the treatments. The fine-scale temporal changes in microRNA expression highlighted the importance of time-series sampling in identifying stress-responsive microRNAs and analyzing their role in stress response/tolerance.

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects

“…miRNAs have an active role in response to flooding in plants as revealed by genome-wide studies in response to hypoxia (Moldovan et al, 2010; Licausi et al, 2011b), waterlogging (Liu et al, 2012; Zhai et al, 2013), and submergence (Zhang et al, 2008; Jeong et al, 2013; Jin et al, 2017; Li et al, 2017; Franke et al, 2018). Despite the fact that reports of miRNA’s responsiveness to flooding stress are still scarce in comparison to reports on other abiotic stress, existing studies have revealed that miRNAs regulate four main lines of response to flooding stress including morphological adaptation, management of energy supply, control of flowering, and oxidative stress response (Figure 2).…”

“…Based on the previous knowledge that miR167 controls the expression of ARFs to regulate adventitious and lateral root development (Gutierrez et al, 2009), regulation of ARFs by miR167 in maize roots could have a balancing effect between suppressing primary root growth and promoting adventitious rooting in response to flooding in a time-scale manner. MiR167 was also up-regulated in the internodes of Alternanthera plants (Li et al, 2017) and Populus seedlings (Ren et al, 2012) and down-regulated in Lotus seedlings under submersion (Jin et al, 2017), probably to control some of the diverse roles of ARF transcription factors in different tissues (i.e., shoot/petiole elongation) in response to flooding.…”

“…Fine-temporal regulation of miRNAs is important for the response to flooding stress. Many miRNAs show fluctuating expression profiles during the time-course of hypoxia or submergence treatments (Licausi et al, 2011b; Li et al, 2017). In maize roots, long- and short-term waterlogging accumulated a series of miRNAs with opposite expression profiles depending on the duration of the stress.…”

“…In some cases, novel non-conserved miRNAs were identified that are responsive to flooding. These miRNAs are interesting because functional characterization has uncovered new functions potentially explaining group or species-specific traits in plants that have not been described in classic model systems (Ren et al, 2012; Jin et al, 2017; Li et al, 2017). In addition, the identification of miRNAs involved in flooding tolerance and differential strategies for tolerance could be facilitated by analysis of the natural variation using different ecotypes with contrasting tolerance to flooding (Liu et al, 2012) and in flooding-tolerant models like Sesbania (Ren et al, 2017), Oryza (Nishiuchi et al, 2012), Rumex , and Rorippa (Voesenek et al, 2014).…”

Co-sequencing and novel delayed anti-correlation identify function for pancreatic enriched microRNA biomarkers in a rat model of acute pancreatic injury

“…These single time points have been logically chosen to provide the largest opportunity to capture relevant data but do not attempt to identify temporal relationships. Those studies that examine time series data [ 64 , 65 ] rely upon intra-time point comparisons with the advantage of assessing changes for individual molecules from time point to time point but do not address how a change in one entity at one time point might impact a different entity at a different time point. The present study includes very acute time points, 1 h, 3 h, and 6 h, as well as time points 24 and 48 h post-treatment.…”