Integrated transcriptome, small RNA, and degradome analysis to elucidate the regulation of rice seedling mesocotyl development during the passage from darkness to light

The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the uniform emergence of direct-seeded rice.Its elongation is inhibited by light and induced in darkness.This investigation of an indica rice(P25)with vigorous mesocotyl elongation was aimed at identifying the"omics"basis of its lightinduced growth inhibition.A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes(DEGs)and differentially abundant micro RNAs(mi RNAs).Degradome sequencing analysis revealed 27 negative mi RNA-target pairs.A co-expression regulatory network was constructed based on the mi RNAs,their corresponding targets,and DEGs with a common Gene Ontology term.It suggested that auxin and light,probably antagonistically,affect mesocotyl elongation by regulating polyamine oxidase activity.

Transcriptome and degradome sequencing reveals changes in Populus×euramericana‘Neva’caused by its allelopathic response to p-hydroxybenzoic acid

Plant species produce different types of allelopathic chemicals in nature;however,little is known about the differential regulation of plant allelopathy.Because allelopathy caused by p-hydroxybenzoic acid(pHBA)is one of the main obstacles to continuous cropping of Populus×euramericana ‘Neva’,we examined gene expression dynamics in Neva leaves induced by pHBA.The expression of genes related to photosynthesis and respiration changed,while mRNA involved in regulating gene expression during allelopathy was degraded.Some miRNAs that are involved in plant allelopathy target crucial genes for regulating reactive oxygen species.Moreover,coexpression regulatory networks were constructed based on profiles of the identified miRNA-target interactions and the differentially expressed miRNA-target pairs.These findings provide a mechanistic framework for understanding allelopathy in plants.

Analyses of a Glycine max Degradome Library Identify microRNA Targets and MicroRNAs that Trigger Secondary SiRNA Biogenesis

Plant microRNAs （miRNAs） regulate gene expression mainly by guiding cleavage of target mRNAs. In this study, a degradome library constructed from different soybean （Glycine max （L.） Merr.） tissues was deep-sequenced. 428 potential targets of small interfering RNAs and 25 novel miRNA families were identified. A total of 211 potential miRNA targets, including 174 conserved miRNA targets and 37 soybean- specific miRNA targets, were identified. Among them, 121 targets were first discovered in soybean. The signature distribution of soybean primary miRNAs （pri-miRNAs） showed that most pri-miRNAs had the characteristic pattern of Dicer processing. The biogenesis of TAS3 small interfering RNAs （siRNAs） was conserved in soybean, and nine Auxin Response Factors were identified as TAS3 siRNA targets. Twenty- three miRNA targets produced secondary small interfering RNAs （siRNAs） in soybean. These targets were guided by five miRNAs： gma-miR393, gma-miR1508, gma-miR1510, gma-miR1514, and novel-11. Multiple targets of these secondary siRNAs were detected. These 23 miRNA targets may be the putative novel TAS genes in soybean. Global identification of miRNA targets and potential novel TAS genes will nnntrihnltp, tn r~__~nrP.h nn th~ f, mP.tinn_~ nf miRNA~ in ~nvh^n

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.

Characterization and function of Tomato yellow leaf curl virus-derived small RNAs generated in tolerant and susceptible tomato varieties

supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China （20134320120013）;the Natural Science Foundation of Hunan Province, China （14JJ3095）

Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo(Phyllostachys edulis)

Circular RNAs(circRNAs)are endogenous non-coding RNAs with covalently closed structures,which have important functions in plants.However,their biogenesis,degradation,and function upon treatment with gibberellins(GAs)and auxins(1-naphthaleneacetic acid,NAA)remain unknown.Here,we systematically identified and characterized the expression patterns,evolutionary conservation,genomic features,and internal structures of circRNAs using RNase R-treated libraries from moso bamboo(Phyllostachys edulis)seedlings.Moreover,we investigated the biogenesis of circRNAs dependent on both cis-and trans-regulation.We explored the function of circRNAs,including their roles in regulating microRNA(miRNA)-related genes and modulating the alternative splicing of their linear counterparts.Importantly,we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs.Finally,we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA.Collectively,our study provides insights into the biogenesis,function,and miRNA-mediated degradation of circRNAs in moso bamboo.

Multiomics analysis provides new insights into the regulatory mechanism of carotenoid biosynthesis in yellow peach peel

Carotenoids,as natural tetraterpenes,play a pivotal role in the yellow coloration of peaches and contribute to human dietary health.Despite a relatively clear understanding of the carotenoid biosynthesis pathway,the regulatory mechanism of miRNAs involved in carotenoid synthesis in yellow peaches remain poorly elucidated.This study investigated a total of 14 carotenoids and 40 xanthophyll lipids,including six differentially accumulated carotenoids:violaxanthin,neoxanthin,lutein,zeaxanthin,cryptoxanthin,and(E/Z)-phytoene.An integrated analysis of RNA-seq,miRNA-seq and degradome sequencing revealed that miRNAs could modulate structural genes such as PSY2,CRTISO,ZDS1,CHYB,VDE,ZEP,NCED1,NCED3 and the transcription factors NAC,ARF,WRKY,MYB,and bZIP,thereby participating in carotenoid biosynthesis and metabolism.The authenticity of miRNAs and target gene was corroborated through quantitative real-time PCR.Moreover,through weighted gene coexpression network analysis and a phylogenetic evolutionary study,coexpressed genes and MYB transcription factors potentially implicated in carotenoid synthesis were identified.The results of transient expression experiments indicated that mdm-miR858 inhibited the expression of PpMYB9 through targeted cleavage.Building upon these findings,a regulatory network governing miRNA-mediated carotenoid synthesis was proposed.In summary,this study comprehensively identified miRNAs engaged in carotenoid biosynthesis and their putative target genes,thus enhancing the understanding of carotenoid accumulation and regulatory mechanism in yellow peach peel and expanding the gene regulatory network of carotenoid synthesis.