Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids

(2019) Robert G. Latta et al.   Scientific Reports

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

Haplotype-based genotyping-by-sequencing in oat genome research

(2018) Wubishet A. Bekele et al.   PLANT BIOTECHNOLOGY JOURNAL

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications

(2017) Robert J. Soreng et al.   Journal of Systematics and Evolution

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Genome-Wide Association Mapping of Crown Rust Resistance in Oat Elite Germplasm

(2017) Kathy Esvelt Klos et al.   Plant Genome

Genomic abundance is not predictive of tandem repeat localization in grass genomes

(2017) Paul Bilinski et al.   PLoS One

Enhancing crop yield by optimizing plant developmental features

(2016) Jyotirmaya Mathan et al.   DEVELOPMENT

Genome size variation in the genus Avena

(2016) Honghai Yan et al.   GENOME

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

(2016) David John Bertioli et al.   NATURE GENETICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

(2016) Honghai Yan et al.   THEORETICAL AND APPLIED GENETICS

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

(2016) Ashley S. Chaffin et al.   Plant Genome

Comparative Analysis of GC Content Variations in Plant Genomes

(2016) Ratnesh Singh et al.   Tropical Plant Biology

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

(2015) Eva-Maria Willing et al.   Nature Plants

Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae)

(2014) Aretuza Sousa et al.   ANNALS OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Plant genome size variation: bloating and purging DNA

(2014) T. P. Michael   Briefings in Functional Genomics

Genetic analysis for fodder yield and other important traits in oats (Avena sativaL.)

(2014) Mushtaq Ahmad et al.   INDIAN JOURNAL OF GENETICS AND PLANT BREEDING

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Chromosome location and allele-specific PCR markers for marker-assisted selection of the oat crown rust resistance gene Pc91

(2013) B. N. Gnanesh et al.   MOLECULAR BREEDING

Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses

(2013) Miguel Minaya et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

(2013) Rebekah E. Oliver et al.   PLoS One

Molecular Dating, Evolutionary Rates, and the Age of the Grasses

(2013) P.-A. Christin et al.   SYSTEMATIC BIOLOGY

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Oat Beta-Glucan: Its Role in Health Promotion and Prevention of Diseases

(2012) Cheickna Daou et al.   COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY

Avena sativa(Oat), A Potential Neutraceutical and Therapeutic Agent: An Overview

(2012) Rajinder Singh et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Virulence in Oat Crown Rust (Puccinia coronata f. sp. avenae) in the United States from 2006 through 2009

(2011) M. L. Carson   PLANT DISEASE

New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.

(2011) R. E. Oliver et al.   THEORETICAL AND APPLIED GENETICS

Asymmetric Distribution of Gene Expression in the Centromeric Region of Rice Chromosome 5

(2011) Hiroshi Mizuno et al.   Frontiers in Plant Science

Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time

(2010) YANIS BOUCHENAK-KHELLADI et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

New hypotheses for the health-protective mechanisms of whole-grain cereals: what is beyond fibre?

(2010) Anthony Fardet   NUTRITION RESEARCH REVIEWS

Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison

(2010) Jianchang Du et al.   PLANT JOURNAL

Mapping of the oat crown rust resistance gene Pc91

(2010) C. A. McCartney et al.   THEORETICAL AND APPLIED GENETICS

A new chromosome nomenclature system for oat (Avena sativa L. and A. byzantina C. Koch) based on FISH analysis of monosomic lines

(2010) M. J. Sanz et al.   THEORETICAL AND APPLIED GENETICS

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

Centromeres Convert but Don't Cross

(2010) Paul B. Talbert et al.   PLOS BIOLOGY

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

(2009) Z. Tian et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Catastrophic flood of the Mediterranean after the Messinian salinity crisis

(2009) D. Garcia-Castellanos et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

Avenanthramides, polyphenols from oats, exhibit anti-inflammatory and anti-itch activity

(2008) Runa Sur et al.   ARCHIVES OF DERMATOLOGICAL RESEARCH

Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes

(2008) O. Raskina et al.   CYTOGENETIC AND GENOME RESEARCH

Climate-Driven Ecosystem Succession in the Sahara: The Past 6000 Years

(2008) S. Kro pelin et al.   SCIENCE