title: NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes.
abstract: Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip.
authors: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.
authors: Dongliang
authors: D
authors: Yu
authors: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors: Yijun
authors: Y
authors: Meng
authors: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors: Ziwei
authors: Z
authors: Zuo
authors: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors: Jie
authors: J
authors: Xue
authors: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China.|Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
authors: Huizhong
authors: H
authors: Wang
mesh_terms: D031667:Dendrobium / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D034741:RNA, Small Interfering / Q000096:biosynthesis / Q000235:genetics; D059467:Transcriptome / Q000502:physiology*
chemical_list: D018749:RNA, Plant; D034741:RNA, Small Interfering