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

The Integrated mRNA and miRNA Approach Reveals Potential Regulators of Flowering Time in Arundina graminifolia

Orchids are among the most precious flowers in the world. Regulation of flowering time is one of the most important targets to enhance their ornamental value. The beauty of Arundina graminifolia is its year-round flowering, although the molecular mechanism of this flowering ability remains masked. Therefore, we performed a comprehensive assessment to integrate transcriptome and miRNA sequencing to disentangle the genetic regulation of flowering in this valuable species. Clustering analyses provided a set of molecular regulators of floral transition and floral morphogenesis. We mined candidate floral homeotic genes, including FCA, FPA, GI, FT, FLC, AP2, SOC1, SVP, GI, TCP, and CO, which were targeted by a variety of miRNAs. MiR11091 targeted the highest number of genes, including candidate regulators of phase transition and hormonal control. The conserved miR156-miR172 pathway of floral time regulation was evident in our data, and we found important targets of these miRNAs in the transcriptome. Moreover, endogenous hormone levels were determined to decipher the hormonal control of floral buds in A. graminifolia. The qRT-PCR analysis of floral and hormonal integrators validated the transcriptome expression. Therefore, miRNA-mediated mining of candidate genes with hormonal regulation forms the basis for comprehending the complex regulatory network of perpetual flowering in precious orchids. The findings of this study can do a great deal to broaden the breeding programs for flowering time manipulation of orchids.

Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Carya cathayensis Sarg.)

Hickory, an endemic woody oil and fruit tree species in China, is of great economic value. However, hickory has a long juvenile period and an inconsistent flowering of males and females, thus influencing the bearing rates and further limiting fruits yield. Currently, it is reported that long noncoding RNAs (lncRNAs) play critical regulatory roles in biological processes. However, the role of lncRNAs in the development of hickory female flowers remains unclear. In this study, a total of 6,862 putative lncRNAs were identified from the female flower transcriptomes in three different growth stages of hickory. We proposed that lncRNAs might play an important role in phytohormone signaling processes for flower formation, especially in the abscisic acid and jasmonic acid pathways, according to the results of our Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Moreover, we predicted the interactions among four microRNAs (miRNAs), three lncRNAs, and four genes. We proposed that facing the changing environment, LNC_002115 competes with PHOSPHATE2 (PHO2) for the binding sites on cca-miR399f, and protects PHO2 from suppression. In addition, cis-acting LNC_002115 regulates the expression of the SHORT VEGETATIVE PHASE (SVP) by influencing ABRE-binding factor (ABF). In brief, LNC_002115 regulates hickory female floral development by impacting both PHO2 and SVP. This study was the first to identify lncRNAs involved in hickory female floral development, and provided new insight to elucidate how lncRNAs and their targets play a role in female floral development in hickory, thus unfolding the opportunities for functional characterization of blossom-related lncRNAs in further studies.

The Genetic and Hormonal Inducers of Continuous Flowering in Orchids: An Emerging View

Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.

Global Transcriptome Analysis Revealed the Molecular Regulation Mechanism of Pigment and Reactive Oxygen Species Metabolism During the Stigma Development of Carya cathayensis

Hickory (Carya cathayensis Sarg.) is a monoecious plant of the genus Carya of the Juglandaceae family. Its nuts contain a number of nutritional compounds and are deeply loved by consumers. Interestingly, it was observed that the color of hickory stigma changed obviously from blooming to mature. However, the molecular mechanism underlying color formation during stigma development and the biological significance of this phenomenon was mostly unknown. In this work, pigment content, reactive oxygen species (ROS) removal capacity, and transcriptome analysis of developing stigma of hickory at 4 differential sampling time points (S1, S2, S3, and S4) were performed to reveal the dynamic changes of related pigment, antioxidant capacity, and its internal molecular regulatory mechanism. It was found that total chlorophyll content was decreased slightly from S1 to S4, while total carotenoids content was increased from S1 to S3 but decreased gradually from S3 to S4. Total anthocyanin content continued to increase during the four periods of stigma development, reaching the highest level at the S4. Similarly, the antioxidant capacity of stigma was also gradually improved from S1 to S4. Furthermore, transcriptome analysis of developing hickory stigma identified 31,027 genes. Time-series analysis of gene expressions showed that these genes were divided into 12 clusters. Cluster 5 was enriched with some genes responsible for porphyrin and chlorophyll metabolism, carotenoid metabolism, and photosynthesis. Meanwhile, cluster 10 was enriched with genes related to flavonoid metabolism, including anthocyanin involved in ROS scavenging, and its related genes were mainly distributed in cluster 12. Based on the selected threshold values, a total of 10432 differentially expressed genes were screened out and enriched in the chlorophyll, carotenoid, anthocyanin, and ROS metabolism. The expression trends of these genes provided plausible explanations for the dynamic change of color and ROS level of hickory stigma with development. qRT-PCR analyses were basically consistent with the results of RNA-seq. The gene co-regulatory networks of pigment and ROS metabolism were further constructed and MYB113 (CCA0887S0030) and WRKY75 (CCA0573S0068) were predicted to be two core transcriptional regulators. These results provided in-depth evidence for revealing the molecular mechanism of color formation in hickory stigma and its biological significance.

Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

MicroRNAs in Woody Plants

MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.

A potential endogenous gibberellin-mediated signaling cascade regulated floral transition in Magnolia × soulangeana 'Changchun'

The floral transition is a critical developmental switch in plants, and has profound effects on the flower production and yield. Magnolia × soulangeana 'Changchun' is known as a woody ornamental plant, which can bloom in spring and summer, respectively. In this study, anatomical observation, physiological measurement, transcriptome, and small RNA sequencing were performed to investigate potential endogenous regulatory mechanisms underlying floral transition in 'Changchun'. Transition of the shoot apical meristem from vegetative to reproductive growth occurred between late April and early May. During this specific developmental process, a total of 161,645 unigenes were identified, of which 73,257 were significantly differentially expressed, while a number of these two categories of miRNAs were 299 and 148, respectively. Further analysis of differentially expressed genes (DEGs) revealed that gibberellin signaling could regulate floral transition in 'Changchun' in a DELLA-dependent manner. In addition, prediction and analysis of miRNA targeted genes suggested that another potential molecular regulatory module was mediated by the miR172 family and other several novel miRNAs (Ms-novel_miR139, Ms-novel_miR229, and Ms-novel_miR232), with the participation of up- or down-regulating genes, including MsSVP, MsAP2, MsTOE3, MsAP1, MsGATA6, MsE2FA, and MsMDS6. Through the integrated analysis of mRNA and miRNA, our research results will facilitate the understanding of the potential molecular mechanism underlying floral transition in 'Changchun', and also provide basic experimental data for the plant germplasm resources innovation in Magnolia.

Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering

Non-coding RNAs with lengths greater than 200 bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < - 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.

Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process

BACKGROUND

Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level.

RESULTS

A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process.

CONCLUSIONS

Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.

Selection of suitable candidate genes for miRNA expression normalization in Yellow River Carp (Cyprinus carpio. var)

Yellow River carp is widely cultivated in the world due to its economic value in aquaculture, and the faster growth of females compared to males. It is believed that microRNAs (miRNA) are involved in gonadal differentiation and development. qPCR is the most preferred method for miRNA functional analysis. Reliable reference genes for normalization in qRT-PCR are the key to ensuring the accuracy of this method. The aim of present research was to evaluate as well as identify the efficacy of reference genes for miRNA expression using qRT-PCR in Yellow River carp. Nine ncRNAs (miR-101, miR-23a, let7a, miR-26a, miR-146a, miR-451, U6, 5S, and 18S) were chosen and tested in four sample sets: (1) different tissues in adult carp, (2) different tissues in juvenile carp, (3) different early developmental stages of carp, and (4) different developmental stages of carp gonads. The stability and suitability values were calculated using NormFinder, geNorm, and BestKeeper software. The results showed that 5S was a suitable reference gene in different tissues of adult and juvenile carp. The genes 5S, 18S, and U6 were the most stable reference genes in the early developmental stages of carp. Let-7a and miR-23a were considered as the suitable reference genes in the development of gonads. All these reference genes were subsequently validated using miR-430. The results showed that genes 5S and 18S were the most suitable reference genes to normalize miRNA expression under normal growth conditions in early different developmental stages. The genes Let-7a, and miR-23a were the most suitable in different developmental stages. The present study is the first comprehensive study of the stability of miRNA reference genes in Yellow River carp, providing valuable as well as basic data for investigating more accurate miRNA expression during gonadal differentiation and development of carp.

Identification of browning-related microRNAs and their targets reveals complex miRNA-mediated browning regulatory networks in Luffa cylindrica

As a non-coding and endogenous small RNA, MicroRNA (miRNA) takes a vital regulatory role in plant growth and development. Long-term storage and processing of many fruits and vegetables, including Luffa, are subject to influences from browning, a common post-harvest problem that adversely affects flavor, aroma, and nutritional value. The browning regulatory networks mediated by miRNA, however, remain largely unexplored. For a systematic identification of browning-responsive miRNAs and the targets, we built two RNA libraries from Luffa pulps of near-isogenic line, with resistant and sensitive browning characteristics respectively, and then sequenced them using Solexa high-throughput technology. We consequently identified 179 known miRNAs that represent 17 non-conserved miRNA families and 24 conserved families, as well as 84 potential novel miRNAs, among which 16 miRNAs (eight known and eight novel miRNAs) were found to exhibit significant differential expressions and were thus identified as browning-related miRNAs. We then studied those browning-responsive miRNAs and the corresponding targets with RT-qPCR and finally validated their expression patterns. The results revealed that the expression patterns are specific to plant development stages and the miRNAs are identified with 39 target transcripts, which involve in plant development, defense response, transcriptional regulation, and signal transduction. After characterizing these miRNAs and their targets, we propose a browning regulatory network model of miRNA-mediatation in this paper. The findings of the work are helpful for the understanding of miRNA-mediated regulatory mechanisms of browning in Luffa, and will facilitate genetic improvement of pulp characteristics in Luffa.

Identification of miRNAs Associated with Graft Union Development in Pecan [Carya illinoinensis (Wangenh.) K. Koch]

Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a high-value fruit tree with a long juvenile period. The fruiting process of pecan seedlings can be largely accelerated through grafting. As non-coding small RNAs, plant miRNAs participate in various biological processes through negative regulation of gene expression. To reveal the roles of miRNAs in the graft union development of pecan, four small RNA libraries were constructed from the graft union at days 0, 8, 15, and 30 after grafting. A total of 47 conserved miRNAs belonging to 31 families and 39 novel miRNAs were identified. For identified miRNAs, 584 target genes were bioinformatically predicted, and 266 of them were annotated; 29 miRNAs (including 16 conserved and 13 novel miRNAs) were differentially expressed during the graft process. The expression profiles of 12 miRNA were further validated by quantitative reverse transcription PCR (qRT-PCR). In addition, qRT-PCR revealed that the expression levels of 3 target genes were negatively correlated with their corresponding miRNAs. We found that miRS26 might be involved in callus formation; miR156, miR160, miR164, miR166, and miRS10 might be associated with vascular bundle formation. These results indicate that the miRNA-mediated gene regulations play important roles in the graft union development of pecan.

Identification and Expression of miRNAs Related to Female Flower Induction in Walnut (Juglans regia L.)

Flower induction is an essential stage in walnut (Juglans regia L.) trees, directly affecting yield, yield stability, fruit quality and commodity value. The objective of this study was to identify miRNAs related to female flower induction via high-throughput sequencing and bioinformatics analysis. A total of 123 miRNAs were identified including 51 known miRNAs and 72 novel miRNAs. Differential expression was observed in 19 of the known miRNAs and 34 of the novel miRNAs. Twelve miRNAs were confirmed by RT-qPCR. A total of 1339 target genes were predicted for the differentially expressed miRNAs. The functions of 616 of those target genes had been previously annotated. The target genes of the differentially expressed miRNAs included: (i) floral homeotic protein APETALA 2 (AP2) and ethylene-responsive transcription factor RAP2-7 which were targeted by jre-miRn69; (ii) squamosa promoter-binding protein 1 (SPB1) and various SPLs (squamosa promoter-binding-like protein) which were targeted by jre-miR157a-5p; (iii) various hormone response factors which were targeted by jre-miR160a-5p (ARF18) and jre-miR167a-5p (ARF8) and (iv) transcription factor SCL6 which was targeted by jre-miR171b-3p, jre-miRn46 and jre-miRn49. The KEGG pathway analysis of the target genes indicated that the differentially expressed miRNAs were mainly enriched to ubiquitin mediated proteolysis, RNA degradation and various carbohydrate metabolism pathways. Many miRNAs were detected in J. regia during female flower induction. Some miRNAs (jre-miR157a-5p, jre-miR160a-5p, jre-miR167a-5p, miR171b-3p jre-miRn69 and jre-miRn49) were involved in female flower induction. The results of this experiment will contribute valuable information for further research about the function of miRNAs in flower induction of J. regia and other fruit trees.

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.

The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis

MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA). In silico target prediction identified 519 potential cro-miRNA targets that include several auxin response factors (ARFs). The presence of cleaved transcripts of miRNA-targeted ARFs in C. roseus cells was confirmed by Poly(A) Polymerase-Mediated Rapid Amplification of cDNA Ends (PPM-RACE). We showed that auxin (indole acetic acid, IAA) repressed the expression of key TIA pathway genes in C. roseus seedlings. Moreover, we demonstrated that a miRNA-regulated ARF, CrARF16, binds to the promoters of key TIA pathway genes and repress their expression. The C. roseus miRNAome reported here provides a comprehensive account of the cro-miRNA populations, as well as their abundance and expression profiles in response to MeJA. In addition, our findings underscore the importance of miRNAs in posttranscriptional control of the biosynthesis of specialized metabolites.

Identification and profiling of conserved and novel microRNAs involved in oil and oleic acid production during embryogenesis in Carya cathayensis Sarg

MicroRNAs (miRNAs) are important regulators of plant development and fruit formation. Mature embryos of hickory (Carya cathayensis Sarg.) nuts contain more than 70% oil (comprising 90% unsaturated fatty acids), along with a substantial amount of oleic acid. To understand the roles of miRNAs involved in oil and oleic acid production during hickory embryogenesis, three small RNA libraries from different stages of embryogenesis were constructed. Deep sequencing of these three libraries identified 95 conserved miRNAs with 19 miRNA*s, 7 novel miRNAs (as well as their corresponding miRNA*s), and 26 potentially novel miRNAs. The analysis identified 15 miRNAs involved in oil and oleic acid production that are differentially expressed during embryogenesis in hickory. Among them, nine miRNA sequences, including eight conserved and one novel, were confirmed by qRT-PCR. In addition, 145 target genes of the novel miRNAs were predicted using a bioinformatic approach. Our results provide a framework for better understanding the roles of miRNAs during embryogenesis in hickory.

Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis

MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B. elliptica treatment or B. elliptica infection for 6 and 24 h. By high-throughput sequencing, 71 known miRNAs belonging to 47 conserved families and 24 novel miRNA were identified, of which 18 miRNAs were downreguleted and 13 were upregulated in response to B. elliptica. Moreover, based on the lily mRNA transcriptome, 22 targets for 9 known and 1 novel miRNAs were identified by the degradome sequencing approach. Most target genes for elliptica-responsive miRNAs were involved in metabolic processes, few encoding different transcription factors, including ELONGATION FACTOR 1 ALPHA (EF1a) and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 2 (TCP2). Furthermore, the expression patterns of a set of elliptica-responsive miRNAs and their targets were validated by quantitative real-time PCR. This study represents the first transcriptome-based analysis of miRNAs responsive to B. elliptica and their targets in lily. The results reveal the possible regulatory roles of miRNAs and their targets in B. elliptica interaction, which will extend our understanding of the mechanisms of this disease in lily.

Comparative Proteomic Analysis of the Graft Unions in Hickory (Carya cathayensis) Provides Insights into Response Mechanisms to Grafting Process

Hickory (Carya cathayensis), a tree with high nutritional and economic value, is widely cultivated in China. Grafting greatly reduces the juvenile phase length and makes the large scale cultivation of hickory possible. To reveal the response mechanisms of this species to grafting, we employed a proteomics-based approach to identify differentially expressed proteins in the graft unions during the grafting process. Our study identified 3723 proteins, of which 2518 were quantified. A total of 710 differentially expressed proteins (DEPs) were quantified and these were involved in various molecular functional and biological processes. Among these DEPs, 341 were up-regulated and 369 were down-regulated at 7 days after grafting compared with the control. Four auxin-related proteins were down-regulated, which was in agreement with the transcription levels of their encoding genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the 'Flavonoid biosynthesis' pathway and 'starch and sucrose metabolism' were both significantly up-regulated. Interestingly, five flavonoid biosynthesis-related proteins, a flavanone 3-hyfroxylase, a cinnamate 4-hydroxylase, a dihydroflavonol-4-reductase, a chalcone synthase, and a chalcone isomerase, were significantly up-regulated. Further experiments verified a significant increase in the total flavonoid contents in scions, which suggests that graft union formation may activate flavonoid biosynthesis to increase the content of a series of downstream secondary metabolites. This comprehensive analysis provides fundamental information on the candidate proteins and secondary metabolism pathways involved in the grafting process for hickory.

Genome-Wide Identification and Characterization of MicroRNAs and Target Genes in Lonicera japonica

MiRNAs function in post-transcriptional regulation of gene expression and play very important roles in plant development. Lonicera japonica is one of the important medicinal plants in China. However, few studies on the discovery of conserved and novel miRNAs from L. japonica were reported. In this study, we employed deep sequencing technology to identify miRNAs in leaf and flower tissues of L. japonica. A total of 22.97 million clean reads from flower and leaf tissues were obtained, which generated 146 conserved miRNAs distributed in 20 families and 110 novel miRNAs. Accordingly, 72 differentially expressed miRNAs (P≤0.001) between leaves and flowers and their potential target genes were identified and validated. The qRT-PCR validation showed that majority of the differentially expressed miRNAs showed significant tissue-specific expression in L. japonica. Furthermore, the miRNA-mRNA and mRNA-mRNA regulatory networks were constructed using Cytoscape software. Taken together, this study identified a large number of miRNAs and target genes in L. japonica, which not only provides the first global miRNA expression profiles, but also sheds light on functional genomics research on L. japonica in the future.

MiR169 and its target PagHAP2-6 regulated by ABA are involved in poplar cambium dormancy

Dormancy is an effective strategy for perennial plants in temperate zones to survive the winter stress. MicroRNAs (miRNAs) have been well known as important regulators for various biological processes. In this study, we checked the expression of miR169 members in the cambium zone during dormancy and active growth in poplar and found that they had distinct expression patterns. We identified and characterized a dormancy-specific target gene of miR169, PagHAP2-6. 5' RACE assays confirmed the direct cleavage of PagHAP2-6 mRNA by miR169. The yeast functional complementation analysis showed that PagHAP2-6 was a homolog of Heme Activator Protein2 (HAP2)/Nuclear factor Y-A (NF-YA) transcription factor in poplar. qRT-PCR analysis indicated that PagHAP2-6 was highly expressed in the dormant stage, which was converse to the expression pattern of pag-miR169a, n, and r. In addition, the transcription of PagHAP2-6 was induced by exogenous abscisic acid (ABA), and both over-expression of PagHAP2-6 in Arabidopsis and transient co-expression assays in Nicotiana benthamiana indicated that PagHAP2-6 could increase the resistance to exogenous ABA. Taken together, the results suggested that miR169 and its target PagHAP2-6 regulated by ABA were involved in poplar cambium dormancy, which provided new insights into the regulatory mechanisms of tree dormancy-active growth transition.

Over-Expression of GmGIa-Regulated Soybean miR172a Confers Early Flowering in Transgenic Arabidopsis thaliana

Flowering is a pivotal event in the life cycle of plants. miR172 has been widely confirmed to play critical roles in flowering time control by regulating its target gene expression in Arabidopsis. However, the role of its counterpart in soybean remains largely unclear. In the present study, we found that the gma-miR172a was regulated by a GIGANTEA ortholog, GmGIa, in soybean through miRNA metabolism. The expression analysis revealed that gma-miR172a has a pattern of diurnal rhythm expression and its abundance increased rapidly as plants grew until the initiation of flowering phase in soybean. One target gene of gma-miR172a, Glyma03g33470, was predicted and verified using a modified RLM 5'-RACE (RNA ligase-mediated rapid amplification of 5' cDNA ends) assay. Overexpression of gma-miR172a exhibited an early flowering phenotype and the expression of FT, AP1 and LFY were simultaneously increased in gma-miR172a-transgenic Arabidopsis plants, suggesting that the early flowering phenotype was associated with up-regulation of these genes. The overexpression of the gma-miR172a-resistant version of Glyma03g33470 weakened early flowering phenotype in the toe1 mutant of Arabidopsis. Taken together, our results suggested that gma-miR172a played an important role in GmGIa-mediated flowering by repressing Glyma03g33470, which in turn increased the expression of FT, AP1 and LFY to promote flowering in soybean.

Floral thermogenesis: An adaptive strategy of pollination biology in Magnoliaceae

Floral thermogenesis plays a crucial role in pollination biology, especially in plant–pollinator interactions. We have recently explored how thermogenesis is related to pollinator activity and odour release in Magnolia sprengeri. By analyzing flower temperatures, emission of volatiles, and insect visitation, we found that floral blends released during pistillate and staminate stages were similar and coincided with sap beetle visitation. Thus, odour mimicry of staminate-stage flowers may occur during the pistillate stage and may be an adaptive strategy of Magnolia species to attract pollinators during both stages, ensuring successful pollination. In addition to the biological significance of floral thermogenesis in Magnolia species, we explored the underlying regulatory mechanisms via profiling miRNA expression in M. denudata flowers during thermogenic and non-thermogenic stages. We identified 17 miRNAs that may play regulatory roles in floral thermogenesis. Functional annotation of their target genes indicated that these miRNAs regulate floral thermogenesis by influencing cellular respiration and light reactions. These findings increase our understanding of plant–pollinator interactions and the regulatory mechanisms in thermogenic plants.

Identification of microRNAs and Their Target Genes Explores miRNA-Mediated Regulatory Network of Cytoplasmic Male Sterility Occurrence during Anther Development in Radish (Raphanus sativus L.)

MicroRNAs (miRNAs) are a type of endogenous non-coding small RNAs that play critical roles in plant growth and developmental processes. Cytoplasmic male sterility (CMS) is typically a maternally inherited trait and widely used in plant heterosis utilization. However, the miRNA-mediated regulatory network of CMS occurrence during anther development remains largely unknown in radish. In this study, a comparative small RNAome sequencing was conducted in floral buds of CMS line 'WA' and its maintainer line 'WB' by high-throughput sequencing. A total of 162 known miRNAs belonging to 25 conserved and 24 non-conserved miRNA families were isolated and 27 potential novel miRNA families were identified for the first time in floral buds of radish. Of these miRNAs, 28 known and 14 potential novel miRNAs were differentially expressed during anther development. Several target genes for CMS occurrence-related miRNAs encode important transcription factors and functional proteins, which might be involved in multiple biological processes including auxin signaling pathways, signal transduction, miRNA target silencing, floral organ development, and organellar gene expression. Moreover, the expression patterns of several CMS occurrence-related miRNAs and their targets during three stages of anther development were validated by qRT-PCR. In addition, a potential miRNA-mediated regulatory network of CMS occurrence during anther development was firstly proposed in radish. These findings could contribute new insights into complex miRNA-mediated genetic regulatory network of CMS occurrence and advance our understanding of the roles of miRNAs during CMS occurrence and microspore formation in radish and other crops.

Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae

Background

Micro RNAs are a class of small non coding RNAs of 20–24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing.

Results

In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.

Conclusions

The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2322-6) contains supplementary material, which is available to authorized users.

Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.)

MicroRNAs (miRNAs) play vital regulatory roles in plant growth and development. The phase transition from vegetative growth to flowering is crucial in the life cycle of plants. To date, miRNA-mediated flowering regulatory networks remain largely unexplored in radish. In this study, two small RNA libraries from radish leaves at vegetative and reproductive stages were constructed and sequenced by Solexa sequencing. A total of 94 known miRNAs representing 21 conserved and 13 non-conserved miRNA families, and 44 potential novel miRNAs, were identified from the two libraries. In addition, 42 known and 17 novel miRNAs were significantly differentially expressed and identified as bolting-related miRNAs. RT-qPCR analysis revealed that some miRNAs exhibited tissue- or developmental stage-specific expression patterns. Moreover, 154 target transcripts were identified for 50 bolting-related miRNAs, which were predominately involved in plant development, signal transduction and transcriptional regulation. Based on the characterization of bolting-related miRNAs and their target genes, a putative schematic model of miRNA-mediated bolting and flowering regulatory network was proposed. These results could provide insights into bolting and flowering regulatory networks in radish, and facilitate dissecting the molecular mechanisms underlying bolting and flowering time regulation in vegetable crops.

Characterization and comparative profiling of the small RNA transcriptomes in two phases of flowering in Cymbidium ensifolium

Background

Cymbidium ensifolium is one of the most important ornamental flowers in China, with an elegant shape, beautiful appearance, and a fragrant aroma. Its unique flower shape has long attracted scientists. MicroRNAs (miRNAs) are critical regulators in plant development and physiology, including floral development. However, to date, few studies have examined miRNAs in C. ensifolium.

Results

In this study, we employed Solexa technology to sequence four small RNA libraries from two flowering phases to identify miRNAs related to floral development. We identified 48 mature conserved miRNA and 71 precursors. These conserved miRNA belonged to 20 families. We also identified 45 novel miRNA which includes 21 putative novel miRNAs*, and 28 hairpin forming precursors. Two trans-acting small interfering RNAs (ta-siRNAs) were identified, one of which was homologous to TAS3a1. TAS3a1 belongs to the TAS3 family, which has been previously reported to target auxin response factors (ARF) and be involved in plant growth and floral development. Moreover, we built a C. ensifolium transctriptome database to identify genes targeted by miRNA, which resulted in 790 transcriptomic target unigenes. The target unigenes were annotated with information from the non-redundant (Nr), gene ontology database (GO), eukaryotic orthologous groups (KOGs) and Kyoto encyclopedia of genes and genomes (KEGG) database. The unigenes included MADS-box transcription factors targeted by miR156, miR172 and miR5179, and various hormone responding factors targeted by miR159. The MADS-box transcription factors are well known to determine the identity of flower organs and hormone responding factors involved in floral development. In expression analysis, three novel and four conserved miRNA were differentially expressed between two phases of flowering. The results were confirmed by RNA-seq and qRT-PCR. The differential expression of two miRNA, miR160 and miR396, targeted ARFs and growth regulating factor (GRF), respectively. However, most of these small RNA were clustered in the uncharacterized group, which suggests there may be many novel small non-coding RNAs yet to be discovered.

Conclusion

Our study provides a diverse set of miRNAs related to cymbidium floral development and serves as a useful resource for investigating miRNA-mediated regulatory mechanisms of floral development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1764-1) contains supplementary material, which is available to authorized users.

Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.)

BACKGROUND

Radish (Raphanus sativus L.) is an economically important root vegetable crop, and the taproot-thickening process is the most critical period for the final productivity and quality formation. MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory function in plant growth and development. However, the characterization of miRNAs and their roles in regulating radish taproot growth and thickening remain largely unexplored. A Solexa high-throughput sequencing technology was used to identify key miRNAs involved in taproot thickening in radish.

RESULTS

Three small RNA libraries from 'NAU-YH' taproot collected at pre-cortex splitting stage, cortex splitting stage and expanding stage were constructed. In all, 175 known and 107 potential novel miRNAs were discovered, from which 85 known and 13 novel miRNAs were found to be significantly differentially expressed during taproot thickening. Furthermore, totally 191 target genes were identified for the differentially expressed miRNAs. These target genes were annotated as transcription factors and other functional proteins, which were involved in various biological functions including plant growth and development, metabolism, cell organization and biogenesis, signal sensing and transduction, and plant defense response. RT-qPCR analysis validated miRNA expression patterns for five miRNAs and their corresponding target genes.

CONCLUSIONS

The small RNA populations of radish taproot at different thickening stages were firstly identified by Solexa sequencing. Totally 98 differentially expressed miRNAs identified from three taproot libraries might play important regulatory roles in taproot thickening. Their targets encoding transcription factors and other functional proteins including NF-YA2, ILR1, bHLH74, XTH16, CEL41 and EXPA9 were involved in radish taproot thickening. These results could provide new insights into the regulatory roles of miRNAs during the taproot thickening and facilitate genetic improvement of taproot in radish.

Identification of microRNAs differentially expressed involved in male flower development

Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.

Molecular characterization and expression analysis of the critical floral genes in hickory (Carya cathayensis Sarg.)

The full ORFs of three floral genes in hickory (Carya cathayensis Sarg.), CcAGL24 (the AGAMOUS-LIKE24 homolog), CcSOC1 (the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 homolog) and CcAP1 (the APETALA1 homolog) are derived using a 5' RACE PCR protocol. Through sequence alignment and phylogenetic analysis, it is demonstrated that the three genes belong to the MADS-Box family. According to the evolutionary trees of the three genes, the homologous genes from the same family cluster well together, while those from different orders doesn't match evolutionary regularity of individual organisms. The result of Quantitative RT-PCR analysis shows that the transcriptional levels of the three genes are up-regulated in early stage and down-regulated in late stage in pistillate floral development. However, it takes different time to reach respective expression peak among the three genes. In staminate floral development, the transcription trend of the three genes is up-regulated, subsequently down-regulated, and then up-regulated again. Nevertheless, those trajectories, peaks, expression levels, inflection points are different in pistillate floral development. The result suggests that their functions are different in between pistillate and staminate floral development. The probable ordinal site of the three genes in the flowering network from top down is CcAGL24, CcSOC1, and CcAP1, which is identical to that in herbaceous plants. Moreover, several adverse environmental factors trigger several negative genes and then confine the development of staminate floral buds. Our results suggest the possible relationship among the three critical floral genes and their functions throughout the floral development in hickory.

Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development?

The facility and versatility of microRNAs (miRNAs) to evolve and change likely underlies how they have become dominant constituents of eukaryotic genomes. In this opinion article I propose that trans-acting small interfering RNA gene 4 (TAS4) evolution may be important for biosynthesis of polyphenolics, arbuscular symbiosis, and bacterial pathogen etiologies. Expression-based and phylogenetic evidence shows that TAS4 targets two novel grape (Vitis vinifera L.) MYB transcription factors (VvMYBA6, VvMYBA7) that spawn phased small interfering RNAs (siRNAs) which probably function in nutraceutical bioflavonoid biosynthesis and fruit development. Characterization of the molecular mechanisms of TAS4 control of plant development and integration into biotic and abiotic stress- and nutrient-signaling regulatory networks has applicability to molecular breeding and the development of strategies for engineering healthier foods.

Evolutionary conservation of microRNA regulatory programs in plant flower development

MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. Flowering is critical for the reproduction of angiosperms. Flower development entails the transition from vegetative growth to reproductive growth, floral organ initiation, and the development of floral organs. These developmental processes are genetically regulated by miRNAs, which participate in complex genetic networks of flower development. A survey of the literature shows that miRNAs, their specific targets, and the regulatory programs in which they participate are conserved throughout the plant kingdom. This review summarizes the role of miRNAs and their targets in the regulation of gene expression during the floral developmental phase, which includes the floral transition stage, followed by floral patterning, and then the development of floral organs. The conservation patterns observed in each component of the miRNA regulatory system suggest that these miRNAs play important roles in the evolution of flower development.

Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing

MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs that play significant regulatory roles in plant growth, development, and biotic and abiotic stress responses. To date, a great number of conserved and species-specific miRNAs have been identified in many important plant species such as Arabidopsis, rice and poplar. However, little is known about identification of miRNAs and their target genes in radish (Raphanus sativus L.). In the present study, a small RNA library from radish root was constructed and sequenced using the high-throughput Solexa sequencing. Through sequence alignment and secondary structure prediction, a total of 545 conserved miRNA families as well as 15 novel (with their miRNA* strand) and 64 potentially novel miRNAs were identified. Quantitative real-time PCR (qRT-PCR) analysis confirmed that both conserved and novel miRNAs were expressed in radish, and some of them were preferentially expressed in certain tissues. A total of 196 potential target genes were predicted for 42 novel radish miRNAs. Gene ontology (GO) analysis showed that most of the targets were involved in plant growth, development, metabolism and stress responses. This study represents a first large-scale identification and characterization of radish miRNAs and their potential target genes. These results could lead to the further identification of radish miRNAs and enhance our understanding of radish miRNA regulatory mechanisms in diverse biological and metabolic processes.