Identification and functional prediction of circRNAs in Populus Euphratica Oliv. heteromorphic leaves.

Populus euphratica Oliv. has typical heterophylly. Linear, lanceolate, ovate and broad-ovate leaves appeared in turn from sprouting to development, to maturity. The environmental adaptabilities of P. euphraticas with different leaves were also different. To explore the role of circRNAs on the morphogenesis of P. euphratica heteromorphic leaves (P.hl) and their stress response, the expression profile of circRNAs was analyzed by strand-specific RNA sequencing for the above four kinds of heteromorphic leaves. According to ceRNA hypothesis, 18 differentially expressed cirRNAs (DECs) could influence the expression of 84 mRNAs by antagonizing 23 miRNAs in five sample-pairs. Based on the function of 84 mRNAs, these DECs participate in development process, response to stimulus, response to hormonal et al. Therefore, these circRNAs were involved in the P.hl morphogenesis and stress response by interacting with miRNAs and mRNAs. Our study complemented the genebank of P. euphratica and provided a new strategy for studying leaf development.

Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves.

The SQUAMOSA promoter-binding protein-like (SPL) family play a key role in guiding the switch of plant growth from juvenile to adult phases. Populus euphratica Oliv. exhibit typical heterophylly, and is therefore an ideal model for studying leaf shape development. To investigate the role and regulated networks of SPLs in the morphogenesis of P. euphratica heteromorphic leaves. In this study, 33 P. euphratica SPL (PeuSPL) genes were identified from P. euphratica genome and transcriptome data. Phylogenetic analysis depicted the classification of these SPL genes into two subgroups. The expression profiles and regulatory networks of P. euphratica SPL genes analysis displayed that major P. euphratica SPL family members gradually increases from linear to broad-ovate leaves, and they were involved in the morphogenesis regulation, stress response, transition from vegetative to reproductive growth, photoperiod, and photosynthesis etc. 14 circRNAs, and 33 lncRNAs can promote the expression of 12 of the P. euphratica SPLs by co-decoying miR156 in heteromorphic leaf morphogenesis. However, it was found that the effect of PeuSPL2-4 and PeuSPL9 in leaf shape development was contrasting to their homologous genes of Arabidopsis. Therefore, it was suggested that the SPL family were evolutionarily conserved for regulation growth, but were varies in different plant for regulation of the organ development.

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.

Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis.

The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn as trees develop to maturity. P. euphratica is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophylls, juvenile heterophylls were sampled individually, and then, the expression patterns of miRNAs, mRNAs, lncRNAs and circRNAs were analysed by small RNA sequencing and strand-specific RNA sequencing. We found that 1374 mRNAs, 19 miRNAs, 71 lncRNAs and 2 circRNAs were P. euphratica heterophyll morphogenesis-associated (PHMA) RNAs; among them, 17 PHMA miRNAs could alter the expression of 46 PHMA mRNAs. Furthermore, 11 lncRNAs and 2 circRNAs interacted with 27 PHMA mRNAs according to the ceRNA hypothesis. According to GO and KEGG pathway analysis, PHMA RNAs were mainly involved in metabolism, response to stimulus and developmental processes. Our results indicated that external environmental factors and genetic factors in P. euphratica co-regulated the expression of PHMA RNAs, repressed cell division, reinforced cell growth, and ultimately resulted in the morphogenesis of P. euphratica heterophylls.