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.

An Integrated Workflow for DNA Methylation Analysis

The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our ＂Next-Gen Sequence＂ websites（http：//mpss.udel.edu）,along with small RNA,RNA-seq and other data types.