Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire

(2020) Burkhard Steuernagel et al.   PLANT PHYSIOLOGY

Undesired fertility restoration in msm1 barley associates with two mTERF genes

(2019) Timm Bernhard et al.   THEORETICAL AND APPLIED GENETICS

Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps

(2019) Tingting Zhu et al.   G3-Genes Genomes Genetics

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Tracing the ancestry of modern bread wheats

(2019) Caroline Pont et al.   NATURE GENETICS

Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing

(2019) Jens Keilwagen et al.   Frontiers in Plant Science

Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye (Secale cereale L.)

(2019) Eva-Maria Braun et al.   Frontiers in Plant Science

Genetic transformation of Triticeae cereals – Summary of almost three-decade's development

(2019) Goetz Hensel   BIOTECHNOLOGY ADVANCES

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing

(2018) Mona Schreiber et al.   Evolutionary Applications

High-throughput development of SSR marker candidates and their chromosomal assignment in rye (Secale cereale L.)

(2018) Jianjian Li et al.   PLANT BREEDING

Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function

(2018) Jiorgos Kourelis et al.   PLANT CELL

Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species

(2018) Axel Himmelbach et al.   PLANT JOURNAL

Genomic Analysis and Prediction within a US Public Collaborative Winter Wheat Regional Testing Nursery

(2018) Trevor W. Rife et al.   Plant Genome

Identification of novel C-repeat binding factor (CBF) genes in rye (Secale cereale L.) and expression studies

(2018) Woo Joo Jung et al.   GENE

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Towards a whole-genome sequence for rye (Secale cerealeL.)

(2017) Eva Bauer et al.   PLANT JOURNAL

Copy number variations ofCBFgenes at theFr-A2locus are essential components of winter hardiness in wheat

(2017) Tobias Würschum et al.   PLANT JOURNAL

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Chromosomes 1BS and 1RS for control of male fertility in wheats and triticales with cytoplasms of Aegilops kotschyi, Ae. mutica and Ae. uniaristata

(2017) Adam J. Lukaszewski   THEORETICAL AND APPLIED GENETICS

QTL mapping and comparative genome analysis of agronomic traits including grain yield in winter rye

(2017) Bernd Hackauf et al.   THEORETICAL AND APPLIED GENETICS

Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.)

(2016) D. B. Fowler et al.   PLoS One

Production and cytomolecular identification of new wheat-perennial rye (Secale cereanum) disomic addition lines with yellow rust resistance (6R) and increased arabinoxylan and protein content (1R, 4R, 6R)

(2016) Annamária Schneider et al.   THEORETICAL AND APPLIED GENETICS

Engineering the 1BS chromosome arm in wheat to remove the Rf multi locus restoring male fertility in cytoplasms of Aegilops kotschyi, Ae. uniaristata and Ae. mutica

(2016) Christopher E. Hohn et al.   THEORETICAL AND APPLIED GENETICS

Evolutionary plasticity of restorer-of-fertility-like proteins in rice

(2016) Joanna Melonek et al.   Scientific Reports

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Fine mapping of the first multi-fertility-restoring gene, Rf multi , of wheat for three Aegilops plasmons, using 1BS-1RS recombinant lines

(2015) Koichiro Tsunewaki   THEORETICAL AND APPLIED GENETICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Male Sterility and Fertility Restoration in Crops

(2013) Letian Chen et al.   Annual Review of Plant Biology

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

Reticulate Evolution of the Rye Genome

(2013) M. M. Martis et al.   PLANT CELL

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Development of conserved ortholog set markers linked to the restorer gene Rfp1 in rye

(2012) Bernd Hackauf et al.   MOLECULAR BREEDING

Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research

(2012) Meiping Zhang et al.   Nature Protocols

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative expression of Cbf genes in the Triticeae under different acclimation induction temperatures

(2009) Chiara Campoli et al.   MOLECULAR GENETICS AND GENOMICS

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

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