[Progress in circular RNAs of plants].

Circular RNAs (circRNAs) are covalently closed, conserved single-stranded transcripts that are produced from precursor mRNA (pre-mRNA) back-splicing. They could function as microRNA sponges, interfere with splicing and bind to protein to regulate the expression of parental genes and linear mRNAs. Next-generation RNA sequencing (RNA-seq) has recently shown that the expression of circRNAs is widespread in plants. circRNAs participate in multiple biological processes such as floral development, fruit ripening, and biotic and abiotic stress responses by cell type-specific and tissue-specific expression patterns, indicating that they may play an important role in plant development. In this review, we summarize the current knowledge of plant circRNAs in recent years, including the biogenesis, detection, databases, expression pattern, and potential functions in comparison with animal results to provide new insights for functional research interests of circRNAs in the future.

Genome-wide analysis of miRNAs in Carya cathayensis.

BACKGROUND: MicroRNA (miRNA) plays an important role in plant development regulation. Hickory is an economically important plant in which the amount of flowering determines its production. RESULTS: Here, 51 conserved miRNAs, which belong to 16 families and 195 novel miRNAs were identified in hickory genome. For each conserved miRNA family, we used sequences from hickory and other plants to construct a phylogenetic tree, which shows that each family has members in hickory. Some of the conserved miRNA families (i.e., miR167 and miR397) have more members in hickory than in other plants because of gene expansion. MiR166 exhibited tandem duplication with three copies being observed. Many members of these conserved miRNA families were detected in hickory flowers, and the expression patterns of target genes were opposite to those of the related miRNAs, indicating that miRNAs may have important functions in floral regulation of hickory. CONCLUSIONS: Taken together, a comprehensive analysis was conducted to identify miRNAs produced in hickory flower organs, demonstrating functional conservation and diversity of miRNA families among hickory, Arabidopsis, grape, and poplar.

Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.).

BACKGROUND: Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis. RESULTS: Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better. CONCLUSIONS: Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC' model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.

Discovery and profiling of novel and conserved microRNAs during flower development in Carya cathayensis via deep sequencing.

Hickory (Carya cathayensis Sarg.) is an economically important woody plant in China, but its long juvenile phase delays yield. MicroRNAs (miRNAs) are critical regulators of genes and important for normal plant development and physiology, including flower development. We used Solexa technology to sequence two small RNA libraries from two floral differentiation stages in hickory to identify miRNAs related to flower development. We identified 39 conserved miRNA sequences from 114 loci belonging to 23 families as well as two novel and ten potential novel miRNAs belonging to nine families. Moreover, 35 conserved miRNA*s and two novel miRNA*s were detected. Twenty miRNA sequences from 49 loci belonging to 11 families were differentially expressed; all were up-regulated at the later stage of flower development in hickory. Quantitative real-time PCR of 12 conserved miRNA sequences, five novel miRNA families, and two novel miRNA*s validated that all were expressed during hickory flower development, and the expression patterns were similar to those detected with Solexa sequencing. Finally, a total of 146 targets of the novel and conserved miRNAs were predicted. This study identified a diverse set of miRNAs that were closely related to hickory flower development and that could help in plant floral induction.

cDNA-AFLP analysis of gene expression in hickory (Carya cathayensis) during graft process.

The graft technique is a valid method for propagating plants. A better elucidation of the graft mechanism is helpful in improving the production efficiency and fruit quality in hickory. In this study, cDNA-amplified fragment length polymorphism analysis was used to examine the gene expression in hickory at four time points (at 0, 3, 7 and 14 days) during the graft process. Forty-nine unique genes involved in the graft mechanism were obtained. The expression patterns of these genes were confirmed by real-time reverse transcription-polymerase chain reaction analysis based on 12 selected genes representing different patterns. The 49 genes composed 19 genes of known function, nine genes of unknown function and 21 novel genes. These 19 genes of known functions were involved in the indole-3-acetic acid transport protein, cell cycle, signal transduction, water metabolism, nuclear metabolism, amino acid metabolism, protein metabolism, carbon metabolism and secretion of substances, suggesting that Carya cathayensis Sarg. undergoes a complex metabolism process during the grafting.

Transcriptional profiling by DDRT-PCR analysis reveals gene expression during seed development in Carya cathayensis Sarg.

Hickory (Carya cathayensis Sarg.) seed has one of the highest oil content and is rich in polyunsaturated fatty acids (PUFAs), which kernel is helpful to human health, particularly to human brain function. A better elucidation of lipid accumulation mechanism would help to improve hickory production and seed quality. DDRT-PCR analysis was used to examine gene expression in hickory at thirteen time points during seed development process. A total of 67 unique genes involved in seed development were obtained, and those expression patterns were further confirmed by semi-quantitative RT-PCR and real time RT-PCR analysis. Of them, the genes with known functions were involved in signal transduction, amino acid metabolism, nuclear metabolism, fatty acid metabolism, protein metabolism, carbon metabolism, secondary metabolism, oxidation of fatty acids and stress response, suggesting that hickory underwent a complex metabolism process in seed development. Furthermore, 6 genes related to fatty acid synthesis were explored, and their functions in seed development process were further discussed. The data obtained here would provide the first clues for guiding further functional studies of fatty acid synthesis in hickory.

Effects of potassium supply on limitations of photosynthesis by mesophyll diffusion conductance in Carya cathayensis.

Potassium (K) influences the photosynthesis process in a number of ways; however, the mechanisms underlying the photosynthetic response to differences in K supply are not well understood. Concurrent measurements of gas exchange and chlorophyll fluorescence were made to investigate the effect of K nutrition on photosynthetic efficiency and mesophyll conductance (g(m)) in hickory seedlings (Carya cathayensis Sarg.) in a greenhouse. The results show that leaf K concentrations < 0.7-0.8% appeared to limit the leaf net CO2 assimilation rate (A), and that the relative limitation of photosynthesis due to g(m) and stomatal conductance (g(s)) decreased with increasing supplies of K. However, a sensitivity analysis indicated that A was most sensitive to the maximum carboxylation rate of Rubisco (V(c,max)) and the maximum rate of electron transport (J(max)). These results indicate that the photosynthetic rate is primarily limited by the biochemical processes of photosynthesis (V(c,max) and J(max)), rather than by g(m) and g(s) in K-deficient plants. Additionally, g(m) was closely correlated with g(s) and the leaf dry mass per unit area (M(A)) in hickory seedlings, which indicates that decreased g(m) and g(s) may be a consequence of leaf anatomical adaptation.