Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants

24-nt reproductive phasiRNAs are broadly present in angiosperms

(2019) Rui Xia et al.   Nature Communications

Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing

(2019) Bhavana Bhan et al.   PLoS One

Lineage-Specific Evolved MicroRNAs Regulating NB-LRR Defense Genes in Triticeae

(2019) Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

OUP accepted manuscript

(2018)   DNA RESEARCH

Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome

(2018) Andrew Funk et al.   PLANT JOURNAL

Small RNAs, emerging regulators critical for the development of horticultural traits

(2018) Chengjie Chen et al.   Horticulture Research

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

(2018) Mikhail M. Pooggin   Frontiers in Microbiology

The association of changes in DNA methylation with temperature-dependent sex determination in cucumber

(2017) Yun-Song Lai et al.   JOURNAL OF EXPERIMENTAL BOTANY

tRNA-derived small RNAs target transposable element transcripts

(2017) German Martinez et al.   NUCLEIC ACIDS RESEARCH

Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs

(2017) Yifei Shen et al.   PLANT JOURNAL

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

(2017) Chenxi Xu et al.   Nature Communications

Long-range control of gene expression via RNA-directed DNA methylation

(2017) M. Jordan Rowley et al.   PLoS Genetics

Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent

(2016) Michael Hackenberg et al.   BMC GENOMICS

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways

(2016) Qili Fei et al.   JOURNAL OF EXPERIMENTAL BOTANY

Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing

(2016) Reina Komiya   JOURNAL OF PLANT RESEARCH

Genome-wide characterization of maize small RNA loci and their regulation in the required to maintain repression6-1 (rmr6-1) mutant and long-term abiotic stresses

(2016) Alice Lunardon et al.   PLANT PHYSIOLOGY

Improved Placement of Multi-mapping Small RNAs

(2016) Nathan R. Johnson et al.   G3-Genes Genomes Genetics

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

A dynamic evolutionary and functional landscape of plant phased small interfering RNAs

(2015) Yi Zheng et al.   BMC BIOLOGY

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

(2015) Damien Formey et al.   BMC GENOMICS

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

(2015) Karl F. Erhard et al.   GENETICS

Extensive Families of miRNAs andPHASLoci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants

(2015) Rui Xia et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis

(2015) Michael Freeling et al.   Molecular Plant

Comprehensive Annotation ofPhyscomitrella patensSmall RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants

(2015) Ceyda Coruh et al.   PLANT CELL

Novel and Recently Evolved MicroRNA Clusters Regulate ExpansiveF-BOXGene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

(2015) Rui Xia et al.   PLANT PHYSIOLOGY

High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea

(2015) Sangeeta Srivastava et al.   PLANT SCIENCE

The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs

(2015) Hongtao Hu et al.   PLoS One

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton

(2015) Qingxin Song et al.   PLoS Genetics

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

(2015) Karl F. Erhard et al.   GENETICS

Bioinformatics Analysis of Small RNAs in Pima (Gossypium barbadense L.)

(2015) Hongtao Hu et al.   PLoS One

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

(2014) Qingli Guo et al.   BIOINFORMATICS

Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava

(2014) Jing Xia et al.   BMC GENOMICS

Seeing the forest for the trees: annotating small RNA producing genes in plants

(2014) Ceyda Coruh et al.   CURRENT OPINION IN PLANT BIOLOGY

Identification and characterization of Argonaute gene family and meiosis-enriched Argonaute during sporogenesis in maize

(2014) Lihong Zhai et al.   Journal of Integrative Plant Biology

Roles of small RNAs in plant disease resistance

(2014) Li Yang et al.   Journal of Integrative Plant Biology

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

(2014) Jonathan I. Gent et al.   PLANT CELL

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

(2014) L. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

(2014) M. R. Woodhouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

(2014) Ricardo A. Chávez Montes et al.   Nature Communications

The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling

(2014) Jie Liu et al.   PLoS Genetics

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Genome-Wide Analysis of DNA Methylation in Soybean

(2013) Qing-Xin Song et al.   Molecular Plant

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs

(2013) K. Rogers et al.   PLANT CELL

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

The Arabidopsis Nucleotidyl Transferase HESO1 Uridylates Unmethylated Small RNAs to Trigger Their Degradation

(2012) Yuanyuan Zhao et al.   CURRENT BIOLOGY

Regulation of transposable elements in maize

(2012) Damon Lisch   CURRENT OPINION IN PLANT BIOLOGY

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

(2012) Qi Zheng et al.   PLANT JOURNAL

Dynamic Nucleotide-Binding Site and Leucine-Rich Repeat-Encoding Genes in the Grass Family

(2012) S. Luo et al.   PLANT PHYSIOLOGY

Role of Transposon-Derived Small RNAs in the Interplay between Genomes and Parasitic DNA in Rice

(2012) Misuzu Nosaka et al.   PLoS Genetics

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Evolution of the large genome in Capsicum annuum occurred through accumulation of single-type long terminal repeat retrotransposons and their derivatives

(2011) Minkyu Park et al.   PLANT JOURNAL

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

(2011) A. Si-Ammour et al.   PLANT PHYSIOLOGY

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Arabidopsis lyrataSmall RNAs: TransientMIRNAand Small Interfering RNA Loci within theArabidopsisGenus

(2010) Zhaorong Ma et al.   PLANT CELL

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome-wide profiling of Populus small RNAs

(2009) Daniel Klevebring et al.   BMC GENOMICS

Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules

(2009) C. Lelandais-Briere et al.   PLANT CELL

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

(2008) M. Freeling et al.   GENOME RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conifers have a unique small RNA silencing signature

(2008) E. V. Dolgosheina et al.   RNA

Evolution of plant microRNAs and their targets

(2008) Michael J. Axtell et al.   TRENDS IN PLANT SCIENCE