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Title: Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1501686
Alternate Identifier(s):
OSTI ID: 1545245; OSTI ID: 1559798
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Name: Frontiers in Microbiology Journal Volume: 10; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Media SA
Country of Publication:
Switzerland
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; arbuscular mycorrhizal fungus; ectomycorrhizal fungus; Laccaria; microRNA; mutualistic symbiosis; Populus; Rhizophagus; small RNA

Citation Formats

Mewalal, Ritesh, Yin, Hengfu, Hu, Rongbin, Jawdy, Sara, Vion, Patrice, Tuskan, Gerald A., Le Tacon, François, Labbé, Jessy L., and Yang, Xiaohan. Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis. Switzerland: N. p., 2019. Web. doi:10.3389/fmicb.2019.00515.
Mewalal, Ritesh, Yin, Hengfu, Hu, Rongbin, Jawdy, Sara, Vion, Patrice, Tuskan, Gerald A., Le Tacon, François, Labbé, Jessy L., & Yang, Xiaohan. Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis. Switzerland. doi:10.3389/fmicb.2019.00515.
Mewalal, Ritesh, Yin, Hengfu, Hu, Rongbin, Jawdy, Sara, Vion, Patrice, Tuskan, Gerald A., Le Tacon, François, Labbé, Jessy L., and Yang, Xiaohan. Mon . "Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis". Switzerland. doi:10.3389/fmicb.2019.00515.
@article{osti_1501686,
title = {Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis},
author = {Mewalal, Ritesh and Yin, Hengfu and Hu, Rongbin and Jawdy, Sara and Vion, Patrice and Tuskan, Gerald A. and Le Tacon, François and Labbé, Jessy L. and Yang, Xiaohan},
abstractNote = {},
doi = {10.3389/fmicb.2019.00515},
journal = {Frontiers in Microbiology},
number = ,
volume = 10,
place = {Switzerland},
year = {2019},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.3389/fmicb.2019.00515

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Works referenced in this record:

Hundreds of putatively functional small open reading frames in Drosophila
journal, January 2011


The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
journal, March 2008


RNA silencing in plants
journal, September 2004


PNRD: a plant non-coding RNA database
journal, November 2014

  • Yi, Xin; Zhang, Zhenhai; Ling, Yi
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1162

Expression Pattern Suggests a Role of MiR399 in the Regulation of the Cellular Response to Local Pi Increase During Arbuscular Mycorrhizal Symbiosis
journal, July 2010

  • Branscheid, Anja; Sieh, Daniela; Pant, Bikram Datt
  • Molecular Plant-Microbe Interactions, Vol. 23, Issue 7
  • DOI: 10.1094/MPMI-23-7-0915

Roles of Plant Small RNAs in Biotic Stress Responses
journal, June 2009


Cross-kingdom RNA trafficking and environmental RNAi for powerful innovative pre- and post-harvest plant protection
journal, August 2017


Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi
journal, June 2005

  • Akiyama, Kohki; Matsuzaki, Ken-ichi; Hayashi, Hideo
  • Nature, Vol. 435, Issue 7043
  • DOI: 10.1038/nature03608

Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
journal, March 2006


A comparison of methods for differential expression analysis of RNA-seq data
journal, March 2013


miR396 affects mycorrhization and root meristem activity in the legume Medicago truncatula
journal, May 2013

  • Bazin, Jérémie; Khan, Ghazanfar Abbas; Combier, Jean-Philippe
  • The Plant Journal, Vol. 74, Issue 6
  • DOI: 10.1111/tpj.12178

The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome
journal, March 2009


Root exudates mediated interactions belowground
journal, October 2014


Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes
journal, May 2018


The microRNA miR171h modulates arbuscular mycorrhizal colonization of Medicago truncatula by targeting NSP2
journal, August 2012


TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013


Impact and Influence of the Natural Vibrio-Squid Symbiosis in Understanding Bacterial–Animal Interactions
journal, December 2016


REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
journal, July 2011


Cell-to-cell and long-distance siRNA movement in plants: mechanisms and biological implications
journal, October 2011

  • Brosnan, Christopher Andrew; Voinnet, Olivier
  • Current Opinion in Plant Biology, Vol. 14, Issue 5
  • DOI: 10.1016/j.pbi.2011.07.011

Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Discovery and revision of Arabidopsis genes by proteogenomics
journal, December 2008

  • Castellana, N. E.; Payne, S. H.; Shen, Z.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 52
  • DOI: 10.1073/pnas.0811066106

Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis
journal, May 2011

  • Devers, Emanuel A.; Branscheid, Anja; May, Patrick
  • Plant Physiology, Vol. 156, Issue 4
  • DOI: 10.1104/pp.111.172627

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs
journal, January 2018

  • Shahid, Saima; Kim, Gunjune; Johnson, Nathan R.
  • Nature, Vol. 553, Issue 7686
  • DOI: 10.1038/nature25027

Auxin Perception Is Required for Arbuscule Development in Arbuscular Mycorrhizal Symbiosis
journal, August 2014

  • Etemadi, Mohammad; Gutjahr, Caroline; Couzigou, Jean-Malo
  • Plant Physiology, Vol. 166, Issue 1
  • DOI: 10.1104/pp.114.246595

A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development
journal, July 2011


Mycorrhization helper bacteria associated with the Douglas fir-Laccaria laccata symbiosis: effects in aseptic and in glasshouse conditions
journal, January 1991


Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release
journal, April 2016

  • Bryan, Anthony C.; Jawdy, Sara; Gunter, Lee
  • Plant Biotechnology Journal, Vol. 14, Issue 10
  • DOI: 10.1111/pbi.12560

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
journal, March 2012


miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
journal, July 2011


Long non-coding RNAs and their functions in plants
journal, October 2015


A modified procedure for staining roots to detect VA mycorrhizas
journal, June 1989


Database resources of the National Center for Biotechnology
journal, January 2003


Emerging evidence for functional peptides encoded by short open reading frames
journal, February 2014

  • Andrews, Shea J.; Rothnagel, Joseph A.
  • Nature Reviews Genetics, Vol. 15, Issue 3
  • DOI: 10.1038/nrg3520

cncRNAs: Bi-functional RNAs with protein coding and non-coding functions
journal, December 2015


Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family
journal, April 2007


Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis
journal, July 2010

  • Bonfante, Paola; Genre, Andrea
  • Nature Communications, Vol. 1, Issue 1
  • DOI: 10.1038/ncomms1046

Small RNAs in development – insights from plants
journal, August 2012


Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides
journal, March 2016


Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes
journal, January 2011


MiR171h restricts root symbioses and shows like its target NSP2 a complex transcriptional regulation in Medicago truncatula
journal, July 2014


Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions: Auxin, plant roots and plant-microbe interaction
journal, December 2012

  • Sukumar, Poornima; LeguÉ, ValÉRie; VayssiÈRes, Alice
  • Plant, Cell & Environment, Vol. 36, Issue 5
  • DOI: 10.1111/pce.12036

Dissecting Arabidopsis lateral root development
journal, April 2003


A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq
journal, March 2016


When one is better than two: RNA with dual functions
journal, April 2011


Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs
journal, June 2009

  • Lanet, Elodie; Delannoy, Etienne; Sormani, Rodnay
  • The Plant Cell, Vol. 21, Issue 6
  • DOI: 10.1105/tpc.108.063412

Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis
journal, March 2017


Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes
journal, May 2014

  • Plett, J. M.; Daguerre, Y.; Wittulsky, S.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 22
  • DOI: 10.1073/pnas.1322671111

Post-transcriptional small RNA pathways in plants: mechanisms and regulations
journal, March 2006


Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
journal, March 2011

  • Yang, X.; Tschaplinski, T. J.; Hurst, G. B.
  • Genome Research, Vol. 21, Issue 4
  • DOI: 10.1101/gr.109280.110

psRNATarget: a plant small RNA target analysis server
journal, May 2011

  • Dai, Xinbin; Zhao, Patrick Xuechun
  • Nucleic Acids Research, Vol. 39, Issue suppl_2
  • DOI: 10.1093/nar/gkr319

LocTree3 prediction of localization
journal, May 2014

  • Goldberg, Tatyana; Hecht, Maximilian; Hamp, Tobias
  • Nucleic Acids Research, Vol. 42, Issue W1
  • DOI: 10.1093/nar/gku396

Small Luggage for a Long Journey: Transfer of Vesicle-Enclosed Small RNA in Interspecies Communication
journal, March 2017


Identification of Arbuscular Mycorrhiza (AM)-Responsive microRNAs in Tomato
journal, March 2016


Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs
journal, October 2004


Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria
journal, May 2017


Phylogenetic tree-informed microRNAome analysis uncovers conserved and lineage-specific miRNAs in Camellia during floral organ development
journal, March 2016

  • Yin, Hengfu; Fan, Zhengqi; Li, Xinlei
  • Journal of Experimental Botany, Vol. 67, Issue 9
  • DOI: 10.1093/jxb/erw095

Long noncoding RNAs: New regulators in plant development
journal, June 2013

  • Zhang, Yu-Chan; Chen, Yue-Qin
  • Biochemical and Biophysical Research Communications, Vol. 436, Issue 2
  • DOI: 10.1016/j.bbrc.2013.05.086

Silencing signals in plants: a long journey for small RNAs
journal, January 2011


A Secreted Fungal Effector of Glomus intraradices Promotes Symbiotic Biotrophy
journal, July 2011


Functions of microRNAs and related small RNAs in plants
journal, May 2006

  • Mallory, Allison C.; Vaucheret, Hervé
  • Nature Genetics, Vol. 38, Issue S6
  • DOI: 10.1038/ng1791

The expanding world of small RNAs
journal, January 2008

  • Großhans, Helge; Filipowicz, Witold
  • Nature, Vol. 451, Issue 7177
  • DOI: 10.1038/451414a

The function of small RNAs in plant biotic stress response: Small RNAs and biotic stress
journal, February 2016

  • Huang, Juan; Yang, Meiling; Zhang, Xiaoming
  • Journal of Integrative Plant Biology, Vol. 58, Issue 4
  • DOI: 10.1111/jipb.12463

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
journal, November 2008


High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes
journal, February 2007


Field response of wheat to arbuscular mycorrhizal fungi and drought stress
journal, August 2003


Current status on role of miRNAs during plant–fungus interaction
journal, January 2014

  • Gupta, Om Prakash; Sharma, Pradeep; Gupta, Raj Kumar
  • Physiological and Molecular Plant Pathology, Vol. 85
  • DOI: 10.1016/j.pmpp.2013.10.002

Variation in the ability to form ectomycorrhizas in the F1 progeny of an interspecific poplar (Populus spp.) cross
journal, March 2001

  • Tagu, D.; Faivre Rampant, Patricia; Lapeyrie, Frédéric
  • Mycorrhiza, Vol. 10, Issue 5
  • DOI: 10.1007/PL00009997

Small open reading frames associated with morphogenesis are hidden in plant genomes
journal, January 2013

  • Hanada, K.; Higuchi-Takeuchi, M.; Okamoto, M.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 6
  • DOI: 10.1073/pnas.1213958110

Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective
journal, May 2013

  • Amaral, P. P.; Dinger, M. E.; Mattick, J. S.
  • Briefings in Functional Genomics, Vol. 12, Issue 3
  • DOI: 10.1093/bfgp/elt016

Long non-coding RNAs as a source of new peptides
journal, September 2014

  • Ruiz-Orera, Jorge; Messeguer, Xavier; Subirana, Juan Antonio
  • eLife, Vol. 3
  • DOI: 10.7554/eLife.03523

Growth stimulation of subterranean clover with vesicular arbuscular mycorrhizas
journal, January 1977

  • Abbott, Lk; Robson, Ad
  • Australian Journal of Agricultural Research, Vol. 28, Issue 4
  • DOI: 10.1071/AR9770639

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


Functional genomics and signaling events in mycorrhizal symbiosis
journal, January 2015


Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq
journal, August 2014

  • Aspden, Julie L.; Eyre-Walker, Ying Chen; Phillips, Rose J.
  • eLife, Vol. 3
  • DOI: 10.7554/eLife.03528

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape
journal, November 2015