Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome

Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies

(2021) Anton Suvorov et al.   SYSTEMATIC BIOLOGY

Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat

(2020) Yunfeng Jiang et al.   NEW PHYTOLOGIST

NLR-Annotator: A Tool for De Novo Annotation of Intracellular Immune Receptor Repertoire

(2020) Wei Zhang   PLANT PHYSIOLOGY

A Collinearity-incorporating Homology Inference Strategy for Connecting Emerging Assemblies in Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

(2020) Yongming Chen et al.   Molecular Plant

Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China

(2020) Chenyang Hao et al.   Molecular Plant

Origin and adaptation to high altitude of Tibetan semi-wild wheat

(2020) Weilong Guo et al.   Nature Communications

Multiple wheat genomes reveal global variation in modern breeding

(2020) Sean Walkowiak et al.   NATURE

A haplotype-led approach to increase the precision of wheat breeding

(2020) Jemima Brinton et al.   Communications Biology

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

(2019) Fei He et al.   NATURE GENETICS

Pervasive hybridizations in the history of wheat relatives

(2019) Sylvain Glémin et al.   Science Advances

Hybridization preceded radiation in diploid wheats

(2019) Stella Huynh et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Genome‐wide sequence information reveals recurrent hybridization among diploid wheat wild relatives

(2019) Nadine Bernhardt et al.   PLANT JOURNAL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

HyDe: A Python Package for Genome-Scale Hybridization Detection

(2018) Paul D Blischak et al.   SYSTEMATIC BIOLOGY

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

(2018) Hong-Qing Ling et al.   NATURE

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B

(2018) Jan Dvorak et al.   THEORETICAL AND APPLIED GENETICS

Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis

(2018) Alevtina S. Ruban et al.   Frontiers in Plant Science

Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops

(2018) Yuka Miki et al.   DNA RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

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

(2017) Ming-Cheng Luo et al.   NATURE

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Reconciling the evolutionary origin of bread wheat (Triticum aestivum )

(2016) Moaine El Baidouri et al.   NEW PHYTOLOGIST

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing

(2015) Xutong Wang et al.   NEW PHYTOLOGIST

PGSB PlantsDB: updates to the database framework for comparative plant genome research

(2015) Manuel Spannagl et al.   NUCLEIC ACIDS RESEARCH

The contribution of wheat to human diet and health

(2015) Peter R. Shewry et al.   Food and Energy Security

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew

(2014) Hong Zhang et al.   BMC GENOMICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The chloroplast view of the evolution of polyploid wheat

(2014) Piotr Gornicki et al.   NEW PHYTOLOGIST

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

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

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation

(2013) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Evolution of Polyploid Triticum Wheats under Cultivation: The Role of Domestication, Natural Hybridization and Allopolyploid Speciation in their Diversification

(2011) Y. Matsuoka   PLANT AND CELL PHYSIOLOGY

Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

(2011) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides

(2008) Jérome Salse et al.   BMC GENOMICS