Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs in the Genesis of Populus euphratica Oliv. Heteromorphic Leaves

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

“…Compared with protein-coding genes, the effect of AS in lncRNAs was much weaker (Tu et al, 2020). Among these lncRNAs, lincRNA accounted for the largest proportion, a finding that was consistent with reports in poplar and hickory (Carya cathayensis) (Liu et al, 2018;Fan et al, 2020;Guo et al, 2020). Studies have revealed that lincRNAs are involved in transcriptional regulation and signal transduction in soybean (Glycine max) and regulate root development in A. thaliana (Li et al, 2016;Golicz et al, 2018).…”

“…However, in other studies, the number of lncRNAs was much more than 183. For example, Liu et al (2018Liu et al ( , 2019 detected 5,952 and 13,099 lncRNAs in poplar, Guo et al (2020) identified 4,460 lncRNAs, and FIGURE 8 | KEGG and GO enrichment analysis of genes co-expressed with two hub TFs. (A,B) KEGG pathway enrichment analysis of genes co-expressed with Lchi05072 and Lchi25777, respectively (only significantly enriched pathways are shown).…”

“…These lncRNAs participate in multiple biological processes, including plant growth and development, the stress response, disease resistance, the immune response, and vernalization response (Liu et al, 2020;Wu et al, 2020); for example, ASCO and COLDAIR participate in Arabidopsis thaliana root development and the vernalization response, respectively (Heo and Sung, 2011;Bardou et al, 2014), ALEX1 enhances rice (Oryza sativa) disease resistance (Yu et al, 2020), and PILNCR1 improves the tolerance of maize (Zea mays) under phosphate deficiency conditions (Du et al, 2018). In our previous study, we identified only 183 lncRNAs that had undergone alternative splicing (AS), and this value was far lower than the number of lncRNAs found in other species (Liu et al, 2018;Guo et al, 2020;Tu et al, 2020). Therefore, it is necessary to comprehensively study lncRNAs in L. chinense.…”

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica

“…To date, most research regarding heterophylly of P. euphratica has focused mainly on leaf morphology, anatomical structure, leaf development, and physiological level ( Zhai et al, 2020 ; Song et al, 2021 ). Some recent studies explored the molecular mechanisms underlying the genesis of P. euphratica heteromorphic leaves through high-throughput sequencing analyses ( Iqbal et al, 2017 ; Qin et al, 2018 ; Zeng et al, 2019 ; Guo et al, 2020 ; Li et al, 2020 ; Fu et al, 2021 ). These studies suggested that specific genes, miRNAs, lncRNAs, and circRNAs may interact with each other in the regulation of leaf morphogenesis in P. euphratica ( Song et al, 2021 ).…”

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

“…In detail, the pseudogenes, mRNAs, lncRNAs, and circRNAs could competitively take the role of ceRNAs via common miRNA response elements (MREs), and thus post-transcriptionally influence the stability and translation of target genes to modulate a broad range of plant morphogenesis and developmental processes [ 4 ]. For example, in Populus euphratica Oliv., morphogenesis-associated ncRNAs acted in the poplar heterophyllous morphogenesis by repressing cell division and reinforcing cell growth [ [1] , [5] , [6] ], and the lncRNA/circRNA-peu-miR396a-PeGRF and lncRNA/circRNA-peu-miR160a-PeARF regulatory (sub) networks affected the maintenance and differentiation of root apical meristems during Populus root development [ 5 ]. In Arabidopsis , an ncRNA ( HIDDEN TREASURE 1 , HID1 ) promoted red light-mediated photomorphogenesis by directly inhibiting PHYTOCHROME-INTERACTING FACTOR 3 , while one key lncRNA, serving as a ceRNA, sequestered miR167 and regulated blue light-directed photomorphogenesis [ 3 ].…”