PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades

Guo, Qingli; Qu, Xiongfei; Jin, Weibo

doi:10.1093/bioinformatics/btu628

Cited by 68 publications

(53 citation statements)

References 20 publications

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“…showed that overexpressed miR482e in potato increased plant sensitivity to Verticillium dahliae infection through NBS-LRR targeting and secondary phasiRNA generation 19 . In a previous study, 90 PHAS loci were predicted using the PhaseTank pipeline on the tomato genome; however, no further analysis for these candidates was presented, such as locus information, chromosome distribution, or experimental evidence 20 . To identify Botrytis cinerea- responsive phasiRNAs in tomato in this study, we used the PhaseTank pipeline for identification of PHAS loci, with two more sRNA datasets (from mock- and B. cinerea -infected tomato leaves) compared to our previous study 20 .…”

Section: Introductionmentioning

confidence: 99%

“…In a previous study, 90 PHAS loci were predicted using the PhaseTank pipeline on the tomato genome; however, no further analysis for these candidates was presented, such as locus information, chromosome distribution, or experimental evidence 20 . To identify Botrytis cinerea- responsive phasiRNAs in tomato in this study, we used the PhaseTank pipeline for identification of PHAS loci, with two more sRNA datasets (from mock- and B. cinerea -infected tomato leaves) compared to our previous study 20 . The candidate genes were also characterized and annotated in terms of overlap with annotated genes, chromosome distribution, and tissue expression.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum

Chen

Tian

et al. 2017

Sci Rep

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Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato, with additional evidence that seven of them can be triggered by five miRNAs. Among the identified loci, 51 were located in genic regions, and the remaining 40 were located in intergenic regions. The transient overexpression of PHAS15 and PHAS26 demonstrated that phasiRNAs predicted by PhaseTank were indeed generated from their respective PHAS loci. Using sRNA-seq data from B. cinerea-infected tomato leaves, we identified 50 B. cinerea-responsive phasiRNAs with increased abundance and five with decreased abundance. Moreover, 164 targets of these differentially expressed phasiRNAs were predicted, and 94 of them were confirmed experimentally using degradome data. Gene ontology analysis of the targets revealed an enrichment of genes with functions related to defense responses and signaling regulation. These results suggest that a large number of endogenous siRNAs, such as phasiRNAs, have not yet been identified in tomato and underscore the urgent need to systematically identify and functionally analyze siRNAs in tomato.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum

Chen

Tian

et al. 2017

Sci Rep

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“… and Guo et al . found 19 PHAS genes and 10 miRNA‐PHAS‐SIR‐transcript regulatory cascades in tomato, respectively.…”

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confidence: 99%

“…Zheng et al (2014) performed a genome-wide discovery of PHAS loci in Chinese sacred lotus and identified a total of 106 PHAS loci [16]. Shivaprasad et al [17] and Guo et al [18] found 19 PHAS genes and 10 miRNA-PHAS-SIR-transcript regulatory cascades in tomato, respectively.…”

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confidence: 99%

Identification of phasiRNAs and their drought‐ responsiveness in Populus trichocarpa

Peng

Liang

et al. 2016

FEBS Letters

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Phased, secondary, small interfering RNA (phasiRNA) perform essential biological functions in plants. However, limited information is available on the role of phasiRNA genes in Populus (poplar), especially during drought stress. In this study, we identified 20 PHAS loci generating 91 phasiRNA in the genome of the model forest tree Populus trichocarpa (P. trichocarpa; western balsam-poplar) using the control and drought libraries. Our analysis indicated that six PHAS (PtPHA14-20) initiated by two Populus-specific miRNAs (miR6445 and miR6427) were specific to Populus. In addition, a total of 47 phasiRNA were found to be drought responsive, and five of them were confirmed by RT-qPCR. The phase cleavage of three PHAS loci by miRNA, and degradation of nine transcript targets by phasiRNA were experimentally confirmed based on degradome data. The identification of these Populus phasiRNA will contribute to a better understanding of their function and regulation during drought stress.

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“…We searched for 24 nt PHAS loci in the A. thaliana genome using small RNA‐seq data. Currently, several distinct algorithms are available to calculate the “phasing” of a sRNA‐producing locus (Dotto et al., ; Guo, Qu, & Jin, ; Zheng, Wang, & Sunkar, ). In general, these algorithms calculate the number of reads that are “in‐phase” against those that are “out‐of‐phase” in order to determine the likelihood that a particular locus truly produces phasiRNAs (Axtell, ).…”

Section: Introductionmentioning

confidence: 99%

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA‐dominated PHAS loci

2018

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Small RNA s regulate key physiological functions in land plants. Small RNA s can be divided into two categories: micro RNA s (mi RNA s) and short interfering RNA s (si RNA s); si RNA s are further subdivided into transposon/repetitive region‐localized heterochromatic si RNA s and phased si RNA s (phasi RNA s). Phasi RNA s are produced from the mi RNA ‐mediated cleavage of a Pol II RNA transcript; the mi RNA cleavage site provides a defined starting point from which phasi RNA s are produced in a distinctly phased pattern. 21–22 nucleotide (nt)‐dominated phasi RNA ‐producing loci ( PHAS ) are well represented in all land plants to date. In contrast, 24 nt‐dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one mi RNA (miR2275) is known to trigger the production of these 24 nt‐dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt‐dominated PHAS loci also exist in Arabidopsis thaliana . We find that highly expressed heterochromatic si RNA s were consistently misidentified as 24 nt‐dominated PHAS loci using multiple PHAS ‐ detecting algorithms. We also find that MIR 2275 is not found in A. thaliana , and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS ‐ detecting algorithms which may lead to false positives when trying to annotate new PHAS , especially 24 nt‐dominated loci.

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PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 68 publications

References 20 publications

Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum

Genome-wide identification and characterization of phased small interfering RNA genes in response to Botrytis cinerea infection in Solanum lycopersicum

Identification of phasiRNAs and their drought‐ responsiveness in Populus trichocarpa

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA‐dominated PHAS loci

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