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Science Bulletin 2024年第6期69卷 784-791页

作者：李冠良陈程杰陈佩珂 Blake C.Meyers 夏瑞 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural UniversityGuangzhou 510640China Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510640China Center Saint LouisMO 63132USA Division of Plant Science and Technology University of Missouri-ColumbiaColumbiaMO 65211USA

Small RNAs(srnas),found extensively in plants,play an essential role in plant growth and *** 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 ***,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 ***,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 *** results showed that srnaminer outperformed these tools in multiple aspects,highlighting its *** 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 ***-srna can display a wealth of srna-specific features,enabling a more comprehensive understanding of srna *** and IGV-srna are both platform-independent software that can be run under all operating *** are now freely available at https://***/kli28/srnaminer and https://***/CJchen/IG V-srna.

关键词： srnaminer srna analysis miRNA PhasiRNA hc-siRNA IGV-srna

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