Species-specific regulatory pathways of small RNAs play sophisticated roles in flower development in Dimocarpus longan Lour.

Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.

Small RNAs, emerging regulators critical for the development of horticultural traits

Small RNAs(sRNAs)have been recently recognized as key genetic and epigenetic regulators in various organisms,ranging from the modification of DNA and histone methylations to the modulation of the abundance of coding or non-coding RNAs.In plants,major regulatory sRNAs are classified as respective microRNA(miRNA)and small interfering RNA(siRNA)species,with the former primarily engaging in posttranscriptional regulation while the latter in transcriptional one.Many of these characterized sRNAs are involved in regulation of diverse biological programs,processes,and pathways in response to developmental cues,environmental signals/stresses,pathogen infection,and pest attacks.Recently,sRNAs-mediated regulations have also been extensively investigated in horticultural plants,with many novel mechanisms unveiled,which display far more mechanistic complexity and unique regulatory features compared to those studied in model species.Here,we review the recent progress of sRNA research in horticultural plants,with emphasis on mechanistic aspects as well as their relevance to trait regulation.Given that major and pioneered sRNA research has been carried out in the model and other plants,we also discuss ongoing sRNA research on these plants.Because miRNAs and phased siRNAs(phasiRNAs)are the most studied sRNA regulators,this review focuses on their biogenesis,conservation,function,and targeted genes and traits as well as the mechanistic relation between them,aiming at providing readers comprehensive information instrumental for future sRNA research in horticulture crops.

Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers

Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities.The biosynthesis of metabolites often exclusively occurs in response to tissue-specific combinatorial developmental cues that are controlled at the transcriptional level.Capsaicinoids are a group of specialized metabolites that confer a pungent flavor to pepper fruits.Capsaicinoid biosynthesis occurs in the fruit placenta and combines its developmental cues.Although the capsaicinoid biosynthetic pathway has been largely characterized,the regulatory mechanisms that control capsaicinoid metabolism have not been fully elucidated.In this study,we combined fruit placenta transcriptome data with weighted gene coexpression network analysis(WGCNA)to generate coexpression networks.A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in pepper.Capsaicinoid biosynthetic gene(CBG)and CaMYB48 expression primarily occurs in the placenta and is consistent with capsaicinoid biosynthesis.CaMYB48 encodes a nucleus-localized protein that primarily functions as a transcriptional activator through its C-terminal activation motif.CaMYB48 regulates capsaicinoid biosynthesis by directly regulating the expression of CBGs,including AT3a and KasIa.Taken together,the results of this study indicate ways to generate robust networks optimized for the mining of CBG-related regulators,establishing a foundation for future research elucidating capsaicinoid regulation.

sRNAanno-a database repository of uniformly annotated small RNAs in plants

Small RNAs(sRNAs)are essential regulatory molecules,and there are three major sRNA classes in plants:microRNAs(miRNAs),phased small interfering RNAs(phased siRNAs or phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).Excluding miRNAs,the other two classes are not well annotated or available in public databases for most sequenced plant genomes.We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available.The results are available via an online repository called sRNAanno(www.plantsRNAs.org).Compared with other public plant sRNA databases,we obtained was much more miRNA annotations,which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations.sRNAanno also provides free access to genomic information for>22,721 PHAS loci and>22 million hc-siRNA loci annotated from these 143 plant species.Both miRNA and PHAS loci can be easily browsed to view their main features,and a collection of archetypal trans-acting siRNA 3(TAS3)genes were annotated separately for quick access.To facilitate the ease of sRNA annotation,sRNAanno provides free service for sRNA annotations to the community.In summary,the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs.

sRNAminer:多功能的植物小RNA分析工具

Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and development.Although various sRNA analysis tools have been developed for plants,the use of most of them depends on programming and command-line environments,which is a challenge for many wet-lab biologists.Furthermore,current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive,normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final results.Here,we present sRNAminer,a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs:microRNAs(miRNAs),phased small interfering RNAs(phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).We constructed a curated or"golden"set of MIRNA and PHAS loci,which was used to assess the performance of sRNAminer in comparison to other existing tools.The results showed that sRNAminer outperformed these tools in multiple aspects,highlighting its functionality.In addition,to enable an efficient evaluation of sRNA annotation results,we developed Integrative Genomics Viewer(IGV)-sRNA,a modified genome browser optimized from IGV and we incorporated it as a functional module in sRNAminer.IGV-sRNA can display a wealth of sRNA-specific features,enabling a more comprehensive understanding of sRNA data.sRNAminer and IGV-sRNA are both platform-independent software that can be run under all operating systems.They are now freely available at https://github.com/kli28/sRNAminer and https://gitee.com/CJchen/IG V-sRNA.

TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining

Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.

Jack of Many Trades: The Multifaceted Role of miR528 in Monocots

MicroRNAs (miRNAs) are essential regulators,involved in almost all aspects of plant growth and development.In plants,miRNAs prese nt in all an giosperms are regarded as con served miRNAs;in contrast,miRNAs restricted to certain lineages (lessconserved) or a single species (species-specific) constitute the non-conserved miRNAs (Cuperus et al.,2011).Different members of a miRNA family usually target similar target genes from a gene family among different species.For in stance,in most analyzed plants,the well-known miR156 family,usually consist!ng of a number of members in a given species,collectively target SQUAMOSA-PROMOTER BINDING PROTEINLIKE (SPL) genes.Gen erally,con served miRNAs target genes encoding transcript factors which function in diverse biological processes.This functional diversity of miRNAs is mainly achieved by the plasticity of their target genes from the same family,such as miR156-targeted SPLs and miR167-targeted ARF (AUXIN RESPONSIVE FACTOR) genes,on regulating distinct downstream gen es.