Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

Version 2.1
Reshetnyak, Ganna; Jacobs, Jonathan M.; Auguy, Florence; Sciallano, Coline; Claude, Lisa; Medina, Clemence; Perez-Quintero, Alvaro J.; Comte, Aurore; Thomas, Emilie; Bogdanove, Adam; Koebnik, Ralf; Szurek, Boris; Dievart, Anne; Brugidou, Christophe; Lacombe, Severine; Cunnac, Sebastien, 2021, "Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"", https://doi.org/10.23708/RXIXM3, DataSuds, V2
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Description

This dataset contains additional supporting information and source code related to the discovery of Xanthomonas-induced small RNAs (xisRNAs) as described in the Related Publication.

Deep small RNA (sRNA) sequencing analysis discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae pathovars. A set of 163 xisRNAs loci were distinctively upregulated in response to various bacterial strains at an early stage of infection. Most xisRNA loci overlap with annotated cis-transcripts sequences often encoding protein kinase domain proteins including RLKs and RLCKs. A number of the corresponding rice cis-genes have documented functions in immune signaling and about one third of the xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. Notably xisRNAs production was dependent on the X. oryzae Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not appear to widely suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify an unrecognized group of unusual sRNAs with a potential role in plant-microbe interactions.

The main entry point for this dataset is the "PHIM_ xisRNA_MS_dataverse_code.html" file that records the code and the output of most secondary analysis computing tasks performed to generate the material relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. Other Files include selected data files that have been used or produced in the course of the analysis workflow.

(2020-02-24)
Subject Agricultural Sciences
Keyword small RNA, Xanthomonas oryzae, rice, plant-microbes interactions
Related Publication An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection Ganna Reshetnyak, Jonathan M Jacobs , Florence Auguy , Coline Sciallano, Lisa Claude, Clemence Medina, Alvaro Perez Quintero , Aurore Comte , Emilie Thomas, Adam J Bogdanove , Ralf Koebnik , Boris Szurek , Anne Dievart , Christophe Brugidou , Severine Lacombe , and Sebastien Cunnac arXiv: BIORXIV/2021/432875
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PHIM_ xisRNA_ancillaryInputData.zip
PHIM_ xisRNA/ZIP Archive - 5.0 MB
Published Mar 5, 2021
6 Downloads
MD5: 8f147c6903729a14cfa76cb3237d17c6
Compressed directory with the gtf file of the MSU7 rice annotation for use in a R session with objects stored in the "session.RData" file.
Data
PHIM_ xisRNA_coveragePlots.zip
PHIM_ xisRNA/ZIP Archive - 31.9 MB
Published Mar 5, 2021
6 Downloads
MD5: 72245fe84113b55b54efa77c44c87308
Compressed directory containing svg image files corresponding to mRNA-seq and sRNA-seq coverage data and annotation for individual xisRNA loci and overlapping rice MSU7 loci displayed at different scales.
Plot
PHIM_ xisRNA_domainsPlots.zip
PHIM_ xisRNA/ZIP Archive - 944.3 KB
Published Mar 5, 2021
4 Downloads
MD5: bd5265d4a84d85a6bc13f363e8f5cb1f
Compressed directory containing svg image files displaying InterProScan results along xisRNA overlapping loci protein product sequences
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PHIM_ xisRNA_iprScan.zip
PHIM_ xisRNA/ZIP Archive - 1.8 MB
Published Mar 5, 2021
4 Downloads
MD5: 5350dacb2c14b070cd1cac19066692b4
Raw output files of the InterProScan search on xisRNA overlapping loci protein product sequences
Data
PHIM_ xisRNA_session.RData
PHIM_ xisRNA/R Data - 849.4 MB
Published Sep 30, 2021
3 Downloads
MD5: d52bc72c86361b747f98eb875e13a00d
R statistical programming language RData file storing the objects created for the production of the "PHIM_ xisRNA_MS_dataverse_code.html" file using the R code found in the html file itself as well as in the "PHIM_ xisRNA_MS_dataverse_code.Rmd" R Markdown file.
Data
PHIM_ xisRNA_xisRNA001_majorUniqueReadsMsa.pdf
PHIM_ xisRNA_xisRNA001_majorUniqueReadsMsa.pdf
PHIM_ xisRNA/Adobe PDF - 38.0 KB
Published Mar 5, 2021
6 Downloads
MD5: e4c59802a37fb02dc0e4ac16e26bdfbb
Multiple sequences alignment of the three most abundant unique read signatures for each strand of the xisRNA001 locus as well as the sequence of the annotated MSU locus transcript in this window.
Documentation
PHIM_ xisRNA_xisRNA002_majorUniqueReadsMsa.pdf
PHIM_ xisRNA_xisRNA002_majorUniqueReadsMsa.pdf
PHIM_ xisRNA/Adobe PDF - 38.9 KB
Published Mar 5, 2021
6 Downloads
MD5: ed792730f5aa2ce95321c2c9f7cc7232
Multiple sequences alignment of the three most abundant unique read signatures for each strand of the xisRNA002 locus as well as the sequence of the annotated MSU locus transcript in this window.
Plot
PHIM_ xisRNA_xisRNA006_majorUniqueReadsMsa.pdf
PHIM_ xisRNA_xisRNA006_majorUniqueReadsMsa.pdf
PHIM_ xisRNA/Adobe PDF - 37.7 KB
Published Mar 5, 2021
6 Downloads
MD5: 43bddb45cbc6c38fd7dda65051be8afa
Multiple sequences alignment of the three most abundant unique read signatures for each strand of the xisRNA006 locus as well as the sequence of the annotated MSU locus transcript in this window.
Plot
PHIM_ xisRNA_xisRNA007_majorUniqueReadsMsa.pdf
PHIM_ xisRNA_xisRNA007_majorUniqueReadsMsa.pdf
PHIM_ xisRNA/Adobe PDF - 38.3 KB
Published Mar 5, 2021
5 Downloads
MD5: dc55589ab73b6ba93f1eecabd4d093fc
Multiple sequences alignment of the three most abundant unique read signatures for each strand of the xisRNA007 locus as well as the sequence of the annotated MSU locus transcript in this window.
Plot
PHIM_ xisRNA_xisRNA009_majorUniqueReadsMsa.pdf
PHIM_ xisRNA_xisRNA009_majorUniqueReadsMsa.pdf
PHIM_ xisRNA/Adobe PDF - 39.3 KB
Published Mar 5, 2021
5 Downloads
MD5: 6c4f17dd6e5181969cca00188faa63e5
Multiple sequences alignment of the three most abundant unique read signatures for each strand of the xisRNA009 locus as well as the sequence of the annotated MSU locus transcript in this window.
Plot
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