The giant diploid faba genome unlocks variation in a global protein crop

The loss of polyphenol oxidase function is associated with hilum pigmentation and has been selected during pea domestication

(2022) Jana Balarynová et al.   NEW PHYTOLOGIST

Combination of electronically driven micromanipulation with laser desorption ionization mass spectrometry – The unique tool for analysis of seed coat layers and revealing the mystery of seed dormancy

(2022) Petra Krejčí et al.   TALANTA

Seed Development and Protein Accumulation Patterns in Faba Bean (Vicia faba, L.)

(2022) Ahmed O. Warsame et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Anatomy and Histochemistry of Seed Coat Development of Wild (Pisum sativum subsp. elatius (M. Bieb.) Asch. et Graebn. and Domesticated Pea (Pisum sativum subsp. sativum L.)

(2021) Lenka Zablatzká et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Chinese pine genome and methylome unveil key features of conifer evolution

(2021) Shihui Niu et al.   CELL

Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology

(2021) Jae Il Lyu et al.   Scientific Reports

Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean (Vicia Faba L.)

(2021) Kedar N. Adhikari et al.   Frontiers in Plant Science

GSAlign: an efficient sequence alignment tool for intra-species genomes

(2020) Hsin-Nan Lin et al.   BMC GENOMICS

Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae

(2020) Laura Ávila Robledillo et al.   MOLECULAR BIOLOGY AND EVOLUTION

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map

(2020) E. Carrillo-Perdomo et al.   Scientific Reports

RNA-directed DNA Methylation

(2020) Robert M. Erdmann et al.   PLoS Genetics

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

(2019) Pavel Neumann et al.   Mobile DNA

Trading on the arbuscular mycorrhiza market: from arbuscules to common mycorrhizal networks

(2019) Daniel Wipf et al.   NEW PHYTOLOGIST

Characterization of repeat arrays in ultra‐long nanopore reads reveals frequent origin of satellite DNA from retrotransposon‐derived tandem repeats

(2019) Tihana Vondrak et al.   PLANT JOURNAL

Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

(2019) Lorenzo Barchi et al.   Frontiers in Plant Science

FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

(2018) Kathrin M Seibt et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate detection of complex structural variations using single-molecule sequencing

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

Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing

(2018) Laura Ávila Robledillo et al.   Scientific Reports

An analysis of the energetic reward offered by field bean (Vicia faba ) flowers: Nectar, pollen, and operative force

(2018) Emily J. Bailes et al.   Ecology and Evolution

DNA methylome analysis provides evidence that the expansion of the tea genome is linked to TE bursts

(2018) Lei Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Seed Storage Proteins of Faba Bean (Vicia faba L): Current Status and Prospects for Genetic Improvement

(2018) Ahmed O. Warsame et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes

(2017) Rosa Maria Cossu et al.   Genome Biology and Evolution

The role of meat in strategies to achieve a sustainable diet lower in greenhouse gas emissions: A review

(2017) John J. Hyland et al.   MEAT SCIENCE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

(2017) Yu-Jian Kang et al.   NUCLEIC ACIDS RESEARCH

Assembly and comparison of two closely related Brassica napus genomes

(2017) Philipp E. Bayer et al.   PLANT BIOTECHNOLOGY JOURNAL

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Grain legume decline and potential recovery in European agriculture: a review

(2016) Peter Zander et al.   Agronomy for Sustainable Development

Simultaneous gene finding in multiple genomes

(2016) Stefanie König et al.   BIOINFORMATICS

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

(2016) Daniel Mapleson et al.   BIOINFORMATICS

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

(2016) Pingchuan Li et al.   BMC GENOMICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies

(2016) Xiaolei Liu et al.   PLoS Genetics

A global experimental dataset for assessing grain legume production

(2016) Charles Cernay et al.   Scientific Data

14,000-year-old seeds indicate the Levantine origin of the lost progenitor of faba bean

(2016) Valentina Caracuta et al.   Scientific Reports

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

(2015) Bernat Gel et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Flanking SNP markers for vicine–convicine concentration in faba bean (Vicia faba L.)

(2015) Hamid Khazaei et al.   MOLECULAR BREEDING

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

(2015) Anne Webb et al.   PLANT BIOTECHNOLOGY JOURNAL

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

Inorganic Nitrogen Uptake and Transport in Beneficial Plant Root-Microbe Interactions

(2014) Pierre Emmanuel Courty et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Curbing global meat consumption: Emerging evidence of a second nutrition transition

(2014) Liesbet Vranken et al.   ENVIRONMENTAL SCIENCE & POLICY

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into Conifer Giga-Genomes

(2014) A. R. De La Torre et al.   PLANT PHYSIOLOGY

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

(2014) Hamid Khazaei et al.   THEORETICAL AND APPLIED GENETICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

BARE Retrotransposons Are Translated and Replicated via Distinct RNA Pools

(2013) Wei Chang et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

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

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

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

(2011) Fabienne Brenet et al.   PLoS One

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Local maternal control of seed size by KLUH/CYP78A5-dependent growth signaling

(2009) N. M. Adamski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE

Global inputs of biological nitrogen fixation in agricultural systems

(2008) David F. Herridge et al.   PLANT AND SOIL