The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

OsADK1, a novel kinase regulating arbuscular mycorrhizal symbiosis in rice

(2022) Rui Guo et al.   NEW PHYTOLOGIST

Conserved and Diverse Transcriptional Reprogramming Triggered by the Establishment of Symbioses in Tomato Roots Forming Arum-Type and Paris-Type Arbuscular Mycorrhizae

(2022) Takaya Tominaga et al.   Plants-Basel

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

(2021) Pawel Sega et al.   BMC GENOMICS

Plant evolution driven by interactions with symbiotic and pathogenic microbes

(2021) Pierre-Marc Delaux et al.   SCIENCE

A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage

(2021) Héctor Montero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lipid exchanges drove the evolution of mutualism during plant terrestrialization

(2021) Mélanie K. Rich et al.   SCIENCE

Important innate differences in determining symbiotic responsiveness in host and non-hosts of arbuscular mycorrhiza

(2021) Shalini Vasan et al.   Scientific Reports

Root cortex development is fine‐tuned by the interplay of MIGs, SCL3 and DELLAs during arbuscular mycorrhizal symbiosis

(2021) Christine Seemann et al.   NEW PHYTOLOGIST

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Conservation and Diversity in Gibberellin-Mediated Transcriptional Responses Among Host Plants Forming Distinct Arbuscular Mycorrhizal Morphotypes

(2021) Takaya Tominaga et al.   Frontiers in Plant Science

The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber

(2020) Jun-Feng Cao et al.   Molecular Plant

A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

(2020) Shengli Yao et al.   PLANT JOURNAL

Functional analysis of the OsNPF4.5 nitrate transporter reveals a conserved mycorrhizal pathway of nitrogen acquisition in plants

(2020) Shuangshuang Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DLK2 regulates arbuscule hyphal branching during arbuscular mycorrhizal symbiosis

(2020) Tania Ho‐Plágaro et al.   NEW PHYTOLOGIST

Rhizospheric Plant–Microbe Interactions: miRNAs as a Key Mediator

(2020) Harriet Middleton et al.   TRENDS IN PLANT SCIENCE

Long non‐coding RNAs associate with jasmonate‐mediated plant defence against herbivores

(2020) Ran Li et al.   PLANT CELL AND ENVIRONMENT

Reconstruction of full-length circular RNAs enables isoform-level quantification

(2019) Yi Zheng et al.   Genome Medicine

Identification and Expression Analysis of GRAS Transcription Factor Genes Involved in the Control of Arbuscular Mycorrhizal Development in Tomato

(2019) Tania Ho-Plágaro et al.   Frontiers in Plant Science

The potassium transporter SlHAK10 is involved in mycorrhizal potassium uptake

(2019) Jianjian Liu et al.   PLANT PHYSIOLOGY

MicroRNAs and Their Regulatory Roles in Plant–Environment Interactions

(2019) Xianwei Song et al.   Annual Review of Plant Biology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses

(2019) Yu Yu et al.   Annual Review of Cell and Developmental Biology

ShinyGO: a graphical gene-set enrichment tool for animals and plants

(2019) Steven Xijin Ge et al.   BIOINFORMATICS

Post-transcriptional Regulation of MicroRNA Accumulation and Function: New Insights from Plants

(2018) Zofia Szweykowska-Kulinska et al.   Molecular Plant

The tomato MAX1 homolog, SlMAX1 , is involved in the biosynthesis of tomato strigolactones from carlactone

(2018) Yanxia Zhang et al.   NEW PHYTOLOGIST

The PILNCR1-miR399 regulatory module is important for low-phosphate tolerance in maize

(2018) Qingguo Du et al.   PLANT PHYSIOLOGY

Alternative Splicing Control of Abiotic Stress Responses

(2018) Tom Laloum et al.   TRENDS IN PLANT SCIENCE

Comparative transcriptome analysis of Poncirus trifoliata identifies a core set of genes involved in arbuscular mycorrhizal symbiosis

(2018) Jianyong An et al.   JOURNAL OF EXPERIMENTAL BOTANY

The MicroRNA319d/TCP10 Node Regulates the Common Bean – Rhizobia Nitrogen-Fixing Symbiosis

(2018) José Á. Martín-Rodríguez et al.   Frontiers in Plant Science

Complex regulation of microRNAs in roots of competitively-grown isogenic Nicotiana attenuata plants with different capacities to interact with arbuscular mycorrhizal fungi

(2018) Priyanka Pandey et al.   BMC GENOMICS

Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

(2018) Yuehui Chao et al.   BMC PLANT BIOLOGY

Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize

(2018) Yunjian Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Medicago AP2-Domain Transcription Factor WRI5a Is a Master Regulator of Lipid Biosynthesis and Transfer during Mycorrhizal Symbiosis

(2018) Yina Jiang et al.   Molecular Plant

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane

(2018) Ronelle Roth et al.   Nature Communications

PlantcircBase: A Database for Plant Circular RNAs

(2017) Qinjie Chu et al.   Molecular Plant

Arbuscular mycorrhiza effects on plant performance under osmotic stress

(2017) Christian Santander et al.   MYCORRHIZA

The rice LysM receptor-like kinase Os CERK1 is required for the perception of short-chain chitin oligomers in arbuscular mycorrhizal signaling

(2017) Gennaro Carotenuto et al.   NEW PHYTOLOGIST

Arbuscular mycorrhiza-specific enzymes FatM and RAM2 fine-tune lipid biosynthesis to promote development of arbuscular mycorrhiza

(2017) Armando Bravo et al.   NEW PHYTOLOGIST

Plant Signaling and Metabolic Pathways Enabling Arbuscular Mycorrhizal Symbiosis

(2017) Allyson M. MacLean et al.   PLANT CELL

The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome

(2017) Agnieszka A. Golicz et al.   PLANT PHYSIOLOGY

Fatty acids in arbuscular mycorrhizal fungi are synthesized by the host plant

(2017) Leonie H. Luginbuehl et al.   SCIENCE

Plants transfer lipids to sustain colonization by mutualistic mycorrhizal and parasitic fungi

(2017) Yina Jiang et al.   SCIENCE

Comparative transcriptome analysis between Solanum lycopersicum L. and Lotus japonicus L. during arbuscular mycorrhizal development

(2017) Yusaku Sugimura et al.   SOIL SCIENCE AND PLANT NUTRITION

Mechanisms Underlying Establishment of Arbuscular Mycorrhizal Symbioses

(2016) Jeongmin Choi et al.   Annual Review of Phytopathology

Symbiotic Fungi Control Plant Root Cortex Development through the Novel GRAS Transcription Factor MIG1

(2016) Carolin Heck et al.   CURRENT BIOLOGY

Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

(2016) Xiao-Ou Zhang et al.   GENOME RESEARCH

Endogenous microRNA sponges: evidence and controversy

(2016) Daniel W. Thomson et al.   NATURE REVIEWS GENETICS

A symbiosis-dedicated SYNTAXIN OF PLANTS 13II isoform controls the formation of a stable host-microbe interface in symbiosis

(2016) Rik Huisman et al.   NEW PHYTOLOGIST

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

(2015) Damien Formey et al.   BMC GENOMICS

From Discovery to Function: The Expanding Roles of Long NonCoding RNAs in Physiology and Disease

(2015) Miao Sun et al.   ENDOCRINE REVIEWS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The LysM receptor-like kinase SlLYK10 regulates the arbuscular mycorrhizal symbiosis in tomato

(2015) Luis Buendia et al.   NEW PHYTOLOGIST

Widespread noncoding circular RNAs in plants

(2015) Chu-Yu Ye et al.   NEW PHYTOLOGIST

Network of GRAS Transcription Factors Involved in the Control of Arbuscule Development inLotus japonicus

(2015) Li Xue et al.   PLANT PHYSIOLOGY

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

Auxin Perception Is Required for Arbuscule Development in Arbuscular Mycorrhizal Symbiosis

(2014) Mohammad Etemadi et al.   PLANT PHYSIOLOGY

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases

(2014) Martina Katharina Ried et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

miR396 affects mycorrhization and root meristem activity in the legumeMedicago truncatula

(2013) Jérémie Bazin et al.   PLANT JOURNAL

A GRAS-Type Transcription Factor with a Specific Function in Mycorrhizal Signaling

(2012) Enrico Gobbato et al.   CURRENT BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Root system architecture: insights from Arabidopsis and cereal crops

(2012) S. Smith et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nonredundant Regulation of Rice Arbuscular Mycorrhizal Symbiosis by Two Members of thePHOSPHATE TRANSPORTER1Gene Family

(2012) Shu-Yi Yang et al.   PLANT CELL

The microRNA miR171h modulates arbuscular mycorrhizal colonization ofMedicago truncatulaby targetingNSP2

(2012) Dominique Lauressergues et al.   PLANT JOURNAL

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

The dawn of symbiosis between plants and fungi

(2011) M. I. Bidartondo et al.   Biology Letters

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Activation of aLotus japonicusSubtilase Gene During Arbuscular Mycorrhiza Is Dependent on the Common Symbiosis Genes and Twocis-Active Promoter Regions

(2011) Naoya Takeda et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Transcription of Two Blue Copper-Binding Protein Isogenes Is Highly Correlated with Arbuscular Mycorrhizal Development inMedicago truncatula

(2010) István Parádi et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Apoplastic plant subtilases support arbuscular mycorrhiza development inLotus japonicus

(2009) Naoya Takeda et al.   PLANT JOURNAL

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

MicroRNA166 controls root and nodule development in Medicago truncatula

(2008) Adnane Boualem et al.   PLANT JOURNAL