Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae)
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae)
Authors
Keywords
-
Journal
PLANT MOLECULAR BIOLOGY
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-11-21
DOI
10.1007/s11103-019-00931-w
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids
- (2019) Paulina Martinez Palacios et al. MOLECULAR BIOLOGY AND EVOLUTION
- Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms
- (2018) Ren Ren et al. Molecular Plant
- Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data
- (2018) Michael J. Axtell et al. PLANT CELL
- Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids
- (2018) Wu Jiao et al. PLANT JOURNAL
- Increased tolerance to organic xenobiotics following recent allopolyploidy in Spartina (Poaceae)
- (2018) Armand Cavé-Radet et al. PLANT SCIENCE
- Transcriptionally active LTR retroelement-related sequences and their relationship with small RNA in moso bamboo (Phyllostachys edulis)
- (2017) Mingbing Zhou et al. MOLECULAR BREEDING
- The evolutionary significance of polyploidy
- (2017) Yves Van de Peer et al. NATURE REVIEWS GENETICS
- 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
- Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)
- (2017) Julie Ferreira de Carvalho et al. PLANT SYSTEMATICS AND EVOLUTION
- Small RNAs: Big Impact on Plant Development
- (2017) Marco D’Ario et al. TRENDS IN PLANT SCIENCE
- The evolutionary origin of plant and animal microRNAs
- (2017) Yehu Moran et al. Nature Ecology & Evolution
- Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and AllododecaploidSpartinaSpecies (Poaceae)
- (2016) Julien Boutte et al. Genome Biology and Evolution
- Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics
- (2016) Donghui Fu et al. PLANT SCIENCE
- Small RNA changes in synthetic Brassica napus
- (2016) Ying Fu et al. PLANTA
- Role of DNA methylation in hybrid vigor inArabidopsis thaliana
- (2016) Takahiro Kawanabe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- miRNAs Are Involved in Determining the Improved Vigor of Autotetrapoid Chrysanthemum nankingense
- (2016) Bin Dong et al. Frontiers in Plant Science
- siRNA-directed DNA Methylation in Plants
- (2015) Meng Xie et al. CURRENT GENOMICS
- Polyploidy and genome evolution in plants
- (2015) Pamela S Soltis et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Silencing of active transposable elements in plants
- (2015) Dalen Fultz et al. CURRENT OPINION IN PLANT BIOLOGY
- Mechanism of siRNA production from repetitive DNA
- (2015) Qiuying Yang et al. GENES & DEVELOPMENT
- MicroRNA: a new target for improving plant tolerance to abiotic stress
- (2015) Baohong Zhang JOURNAL OF EXPERIMENTAL BOTANY
- Differential Expression of miRNAs Under Salt Stress in Spartina alterniflora Leaf Tissues
- (2015) Zuodong Qin et al. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY
- Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel)
- (2015) Hana Zandkarimi et al. MOLECULAR BIOLOGY REPORTS
- Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species
- (2015) Jessica Stapley et al. MOLECULAR ECOLOGY
- The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating
- (2015) M. Rousseau-Gueutin et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Epigenetic Changes in Hybrids
- (2015) Ian K. Greaves et al. PLANT PHYSIOLOGY
- A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in
- (2015) Lei Gong et al. Plant Genome
- Doubling down on genomes: Polyploidy and crop plants
- (2014) Simon Renny-Byfield et al. AMERICAN JOURNAL OF BOTANY
- Nonadditive Gene Expression in Polyploids
- (2014) Mi-Jeong Yoo et al. Annual Review of Genetics
- miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data
- (2014) Jikai Lei et al. BIOINFORMATICS
- A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction
- (2014) Prashant K Srivastava et al. BMC GENOMICS
- The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium
- (2014) Junxing Li et al. BMC PLANT BIOLOGY
- The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra
- (2014) Muhammad Awais Ghani et al. BMC PLANT BIOLOGY
- Small RNAs as important regulators for the hybrid vigour of super-hybrid rice
- (2014) Lei Zhang et al. JOURNAL OF EXPERIMENTAL BOTANY
- PNRD: a plant non-coding RNA database
- (2014) Xin Yi et al. NUCLEIC ACIDS RESEARCH
- Rfam 12.0: updates to the RNA families database
- (2014) Eric P. Nawrocki et al. NUCLEIC ACIDS RESEARCH
- mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat
- (2014) A. Li et al. PLANT CELL
- A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae)
- (2014) Paul M. Peterson et al. TAXON
- Polyploidy and small RNA regulation of cotton fiber development
- (2014) Xueying Guan et al. TRENDS IN PLANT SCIENCE
- Evolutionary history of plant microRNAs
- (2014) Richard S. Taylor et al. TRENDS IN PLANT SCIENCE
- Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome
- (2014) Concepcion M. Diez et al. PLoS Genetics
- Ecological and Evolutionary Misadventures ofSpartina
- (2013) Donald R. Strong et al. Annual Review of Ecology Evolution and Systematics
- Classification and Comparison of Small RNAs from Plants
- (2013) Michael J. Axtell Annual Review of Plant Biology
- RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
- (2013) P. Novak et al. BIOINFORMATICS
- Composition and Expression of Conserved MicroRNA Genes in Diploid Cotton (Gossypium) Species
- (2013) Lei Gong et al. Genome Biology and Evolution
- Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis
- (2013) Guangming He et al. Journal of Genetics and Genomics
- RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond
- (2013) Stephane E. Castel et al. NATURE REVIEWS GENETICS
- Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesizedBrassica napusallotetraploids
- (2013) Véronique Sarilar et al. NEW PHYTOLOGIST
- miRBase: annotating high confidence microRNAs using deep sequencing data
- (2013) Ana Kozomara et al. NUCLEIC ACIDS RESEARCH
- Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis
- (2013) J. Ferreira de Carvalho et al. PLANT MOLECULAR BIOLOGY
- Spatial and temporal expression modes of MicroRNAs in an elite rice hybrid and its parental lines
- (2013) Ruiqiu Fang et al. PLANTA
- Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility
- (2012) Danny W-K Ng et al. CURRENT OPINION IN PLANT BIOLOGY
- Subgenomic analysis of microRNAs in polyploid wheat
- (2012) Melda Kantar et al. FUNCTIONAL & INTEGRATIVE GENOMICS
- Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)
- (2012) J Ferreira de Carvalho et al. HEREDITY
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Homoeolog expression bias and expression level dominance in allopolyploids
- (2012) C. E. Grover et al. NEW PHYTOLOGIST
- MicroRNA Transcriptomic Analysis of Heterosis during Maize Seed Germination
- (2012) Dong Ding et al. PLoS One
- Repeat associated small RNAs vary among parents and following hybridization in maize
- (2012) W. T. Barber et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- ViennaRNA Package 2.0
- (2011) Ronny Lorenz et al. Algorithms for Molecular Biology
- Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants
- (2011) Basel Khraiwesh et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- GC-Content Normalization for RNA-Seq Data
- (2011) Davide Risso et al. BMC BIOINFORMATICS
- Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs
- (2011) Padubidri V Shivaprasad et al. EMBO JOURNAL
- Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs
- (2011) Michal Kenan-Eichler et al. GENETICS
- Ancestral polyploidy in seed plants and angiosperms
- (2011) Yuannian Jiao et al. NATURE
- psRNATarget: a plant small RNA target analysis server
- (2011) Xinbin Dai et al. NUCLEIC ACIDS RESEARCH
- 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
- Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor
- (2011) M. Groszmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
- (2010) Petr Novák et al. BMC BIOINFORMATICS
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- Small RNAs, DNA methylation and transposable elements in wheat
- (2010) Dario Cantu et al. BMC GENOMICS
- Transcriptional activity of transposable elements in maize
- (2010) Carlos M Vicient BMC GENOMICS
- Small RNA-mediated epigenetic modifications in plants
- (2010) Stacey A Simon et al. CURRENT OPINION IN PLANT BIOLOGY
- DNA Methylation Mediated by a MicroRNA Pathway
- (2010) Liang Wu et al. MOLECULAR CELL
- Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae)
- (2010) H. CHELAIFA et al. MOLECULAR ECOLOGY
- Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae)
- (2010) Houda Chelaifa et al. NEW PHYTOLOGIST
- Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
- (2010) G. He et al. PLANT CELL
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen
- (2009) R. Keith Slotkin et al. CELL
- Origin, Biogenesis, and Activity of Plant MicroRNAs
- (2009) Olivier Voinnet CELL
- Origins and Mechanisms of miRNAs and siRNAs
- (2009) Richard W. Carthew et al. CELL
- The allopolyploidArabidopsis kamchaticaoriginated from multiple individuals ofArabidopsis lyrataandArabidopsis halleri
- (2009) RIE SHIMIZU-INATSUGI et al. MOLECULAR ECOLOGY
- Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina
- (2009) Christian Parisod et al. NEW PHYTOLOGIST
- Impact of transposable elements on the organization and function of allopolyploid genomes
- (2009) Christian Parisod et al. NEW PHYTOLOGIST
- 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
- Evolutionary Genetics of Genome Merger and Doubling in Plants
- (2008) Jeff J. Doyle et al. Annual Review of Genetics
- Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)
- (2008) M. L. Ainouche et al. BIOLOGICAL INVASIONS
- Criteria for Annotation of Plant MicroRNAs
- (2008) B. C. Meyers et al. PLANT CELL
- Dual coding of siRNAs and miRNAs by plant transposable elements
- (2008) J. Piriyapongsa et al. RNA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started