Regulatory networks of circRNAs related to transcription factors in Populus euphratica Oliv. heteromorphic leaves

Circular RNAs (circRNAs) are a novel class of non-coding RNAs that are characterized by a covalently closed circular structure. They have been widely found in Populus euphratica Oliv. heteromorphic leaves (P. hl). To study the role of circRNAs related to transcription factors (TFs) in the morphogenesis of P. hl, the expression profiles of circRNAs in linear, lanceolate, ovate, and broad-ovate leaves of P. euphratica were elucidated by strand-specific sequencing. We identified and characterized 22 circRNAs related to TFs in P. hl at the four developmental stages. Using the competing endogenous RNAs hypothesis as a guide, we constructed circRNA–miRNA–TF mRNA regulatory networks, which indicated that circRNAs antagonized microRNAs (miRNAs), thereby influencing the expression of the miRNA target genes and playing a significant role in transcriptional regulation. Gene ontology annotation of the target TF genes predicted that these circRNAs were associated mainly with the regulation of leaf development, leaf morphogenesis, signal transduction, and response to abiotic stress. These findings implied that the circRNAs affected the size and number of cells in P. hl by regulating the expression of TF mRNAs. Our results provide a basis for further studies of leaf development in poplar trees.

Conjoint Analysis of Genome-Wide lncRNA and mRNA Expression of Heteromorphic Leavesin Response to Environmental Heterogeneityin Populus euphratica

Heterophylly is the phenomenon of leaf forms varying along the longitudinal axis within a single plant. Populus euphratica, a heterophyllous woody plant, develops lanceolate leaves and dentate broad-ovate leaves on the bottom and top of the canopy, respectively, which are faced with different intensities of ambient solar radiation. However, the mechanism of the heteromorphic leaf response to the microenvironment in P. euphratica remains elusive. Here, we show that the dentate broad-ovate leaves have advantages in tolerating high light intensity, while lanceolate leaves are excellent at capturing light. Compared with lanceolate leaves, more trichomes, higher stomatal density, thicker lamina, and higher specific leaf weight were observed in dentate broad-ovate leaves. Furthermore, high-throughput RNA sequencing analysis revealed that the expression patterns of genes and long noncoding RNAs (lncRNAs) are different between the two heteromorphic leaves. A total of 36,492 genes and 1725 lncRNAs were detected, among which 586 genes and 54 lncRNAs were differentially expressed. Based on targets prediction, lncRNAs and target genes involved in light adaption, protein repair, stress response, and growth and development pathways were differentially expressed in heteromorphic leaves, 10 pairs of which were confirmed by quantitative real-time PCR. Additionally, the analysis of interactions indicated that lncRNA–mRNA interactions were involved in the response to the microenvironment of heteromorphic leaves. Taken together, these results suggest that the morphological features and joint regulation of lncRNA–mRNA in heteromorphic leaves may serve as survival strategies for P. euphratica, which could lead to optimal utilization of environmental factors.