首页|sRNAminer:A multifunctional toolkit for next-generation sequencing small RNA data mining in plants

sRNAminer:A multifunctional toolkit for next-generation sequencing small RNA data mining in plants

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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 com-parison 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.

sRNAminersRNA analysismiRNAPhasiRNAhc-siRNAIGV-sRNA

Guanliang Li、Chengjie Chen、Peike Chen、Blake C.Meyers、Rui Xia

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State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,College of Horticulture,South China Agricultural University,Guangzhou 510640,China

Guangdong Laboratory for Lingnan Modern Agriculture,South China Agricultural University,Guangzhou 510640,China

Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China,Ministry of Agriculture and Rural Affairs,South China Agricultural University,Guangzhou 510640,China

Donald Danforth Plant Science Center,Saint Louis,MO 63132,USA

Division of Plant Science and Technology,University of Missouri-Columbia,Columbia,MO 65211,USA

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国家自然科学基金国家自然科学基金Key-Area Research and Development Program of Guangdong Provinceopen competition program of top 10 critical priorities of Agricultural Science and Technology Innovation for the 14th Five-YHainan Yazhou Bay Seed LabUS National Science Foundation Award

32072547321023202022B02020700032022SDZG05JBGS-B21HJ00012130883

2024

10.1016/j.scib.2023.12.049

科学通报(英文版)
中国科学院

科学通报(英文版)

CSTPCD
ISSN：1001-6538
年,卷(期)：2024.69(6)
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