The evolutionary history of small RNAs in Solanaceae

Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway

(2021) Kexuan Deng et al.   PeerJ

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

(2020) Alice Lunardon et al.   GENOME RESEARCH

Plant 22-nt siRNAs mediate translational repression and stress adaptation

(2020) Huihui Wu et al.   NATURE

Relationships between genome methylation, levels of non‐coding RNAs, mRNAs and metabolites in ripening tomato fruit

(2020) Jinhua Zuo et al.   PLANT JOURNAL

PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction

(2020) Yuanlong Liu et al.   PLANT CELL

24-nt reproductive phasiRNAs are broadly present in angiosperms

(2019) Rui Xia et al.   Nature Communications

Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato

(2019) Alex Canto-Pastor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Evolution of metabolic novelty: A trichome-expressed invertase creates specialized metabolic diversity in wild tomato

(2019) Bryan J. Leong et al.   Science Advances

Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae

(2019) Pengxiang Fan et al.   CURRENT OPINION IN PLANT BIOLOGY

Next-Generation Sequence Databases: RNA and Genomic Informatics Resources for Plants

(2019) Mayumi Nakano et al.   PLANT PHYSIOLOGY

SonicParanoid: fast, accurate, and easy orthology inference

(2018) Salvatore Cosentino et al.   BIOINFORMATICS

Actions of plant Argonautes: predictable or unpredictable?

(2018) Zeyang Ma et al.   CURRENT OPINION IN PLANT BIOLOGY

OUP accepted manuscript

(2018)   DNA RESEARCH

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

(2018) Michael J. Axtell et al.   PLANT CELL

Dicer-like and RNA-dependent RNA polymerase gene family identification and annotation in the cultivated Solanum tuberosum and its wild relative S. commersonii

(2018) Salvatore Esposito et al.   PLANTA

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening

(2018) Yoshihito Shinozaki et al.   Nature Communications

A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses

(2018) Zhengming Wang et al.   GENES & DEVELOPMENT

Correction: Expansion of Capsicum annum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles

(2018) Dénes Taller et al.   PLoS One

New insights into tomato microRNAs

(2018) Thaís Cunha de Sousa Cardoso et al.   Scientific Reports

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

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

AGO18b negatively regulates determinacy of spikelet meristems on the tassel central spike in maize

(2017) Wei Sun et al.   Journal of Integrative Plant Biology

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

(2017) Jamie Waese et al.   PLANT CELL

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

(2016) Michael A. Hardigan et al.   PLANT CELL

Improved Placement of Multi-mapping Small RNAs

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

Evolution, functions, and mysteries of plant ARGONAUTE proteins

(2015) Han Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae

(2015) Sophie de Vries et al.   Genome Biology and Evolution

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

Nicotiana benthamiana: Its History and Future as a Model for Plant–Pathogen Interactions

(2015) Michael M. Goodin et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Prediction and characterization of Tomato leaf curl New Delhi virus (ToLCNDV) responsive novel microRNAs in Solanum lycopersicum

(2015) Bhubaneswar Pradhan et al.   VIRUS RESEARCH

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

(2014) Qingli Guo et al.   BIOINFORMATICS

miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data

(2014) Jikai Lei et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification of microRNAs in six solanaceous plants and their potential link with phosphate and mycorrhizal signaling

(2014) Mian Gu et al.   Journal of Integrative Plant Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation

(2014) Chao Gao et al.   PLANT BIOTECHNOLOGY JOURNAL

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin 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

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

mirPD: A pattern-based approach for identifying microRNAs from deep sequencing data

(2013) Xiaohan Sun et al.   DIGITAL SIGNAL PROCESSING

EPIGENETIC VARIATION IN ASEXUALLY REPRODUCING ORGANISMS

(2013) Koen J.F. Verhoeven et al.   EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

P-MITE: a database for plant miniature inverted-repeat transposable elements

(2013) Jiongjiong Chen et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots

(2013) Rui Xia et al.   PLANT CELL

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

(2013) Runxuan Zhang et al.   PLoS One

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and Other mRNAs

(2012) P. V. Shivaprasad et al.   PLANT CELL

Genetics and Control of Tomato Fruit Ripening and Quality Attributes

(2011) Harry J. Klee et al.   Annual Review of Genetics

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

(2011) Qing-Xin Song et al.   BMC PLANT BIOLOGY

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

Origin and evolution of SINEs in eukaryotic genomes

(2011) D A Kramerov et al.   HEREDITY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

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

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis

(2010) Josh T Cuperus et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Misexpression of miR482, miR1512, and miR1515 Increases Soybean Nodulation

(2010) H. Li et al.   PLANT PHYSIOLOGY

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

(2010) H.-M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

siRNAs and DNA methylation: seedy epigenetics

(2010) Rebecca A. Mosher et al.   TRENDS IN PLANT SCIENCE

siRNA–Mediated Methylation of Arabidopsis Telomeres

(2010) Jan Vrbsky et al.   PLoS Genetics

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin

(2009) Vera K Schoft et al.   EMBO REPORTS

Rice MicroRNA Effector Complexes and Targets

(2009) L. Wu et al.   PLANT CELL

A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation

(2008) Lucia Daxinger et al.   EMBO JOURNAL

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

(2008) H. Kuang et al.   GENOME RESEARCH