Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea ( Pisum L.)

(2022) Timo Hellwig et al.   PLANT JOURNAL

Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.)

(2021) Arun K. Pandey et al.   THEORETICAL AND APPLIED GENETICS

Panoramic: A package for constructing eukaryotic pan‐genomes

(2021) Lior Glick et al.   Molecular Ecology Resources

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce

(2021) Tong Wei et al.   NATURE GENETICS

Progress in soybean functional genomics over the past decade

(2021) Min Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

A chickpea genetic variation map based on the sequencing of 3,366 genomes

(2021) Rajeev K. Varshney et al.   NATURE

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication

(2020) Yixuan Kou et al.   MOLECULAR BIOLOGY AND EVOLUTION

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Orphan Crops and their Wild Relatives in the Genomic Era

(2020) Chu-Yu Ye et al.   Molecular Plant

Population genetic structure and classification of cultivated and wild pea ( Pisum sp.) based on morphological traits and SSR markers

(2020) Rong Liu et al.   Journal of Systematics and Evolution

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

A reference genome for pea provides insight into legume genome evolution

(2019) Jonathan Kreplak et al.   NATURE GENETICS

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

(2019) Aamir W. Khan et al.   TRENDS IN PLANT SCIENCE

Checking Agriculture’s Pulse: Field Pea (Pisum Sativum L.), Sustainability, and Phosphorus Use Efficiency

(2019) Sarah E. Powers et al.   Frontiers in Plant Science

Resequencing of 683 common bean genotypes identifies yield component trait associations across a north–south cline

(2019) Jing Wu et al.   NATURE GENETICS

LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

(2019) Shujun Ou et al.   Mobile DNA

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Domestication of Pea (Pisum sativum L.): The Case of the Abyssinian Pea

(2018) Norman F. Weeden   Frontiers in Plant Science

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

(2018) James T. Robinson et al.   Cell Systems

Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes

(2018) Vera S. Bogdanova et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Parallel selection on a dormancy gene during domestication of crops from multiple families

(2018) Min Wang et al.   NATURE GENETICS

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

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

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

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic innovation for crop improvement

(2017) Michael W. Bevan et al.   NATURE

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

(2017) Rajeev K Varshney et al.   NATURE GENETICS

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Improvements in Genomic Technologies: Application to Crop Genomics

(2017) Yuxuan Yuan et al.   TRENDS IN BIOTECHNOLOGY

A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.)

(2017) Iveta Hradilová et al.   Frontiers in Plant Science

TACO produces robust multisample transcriptome assemblies from RNA-seq

(2016) Yashar S Niknafs et al.   NATURE METHODS

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

(2016) Mihaela Pertea et al.   Nature Protocols

From Mendel’s discovery on pea to today’s plant genetics and breeding

(2016) Petr Smýkal et al.   THEORETICAL AND APPLIED GENETICS

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean

(2015) Lianjun Sun et al.   NATURE GENETICS

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map

(2015) Nadim Tayeh et al.   PLANT JOURNAL

Genomic Tools in Pea Breeding Programs: Status and Perspectives

(2015) Nadim Tayeh et al.   Frontiers in Plant Science

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

An improved genome release (version Mt4.0) for the model legume Medicago truncatula

(2014) Haibao Tang et al.   BMC GENOMICS

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

(2014) Petr Smýkal et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

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

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

Life cycle and economic assessment of Western Canadian pulse systems: The inclusion of pulses in crop rotations

(2013) S. MacWilliam et al.   AGRICULTURAL SYSTEMS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Crop plants as models for understanding plant adaptation and diversification

(2013) Kenneth M. Olsen et al.   Frontiers in Plant Science

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Review of the health benefits of peas (Pisum sativum L.)

(2012) Wendy J. Dahl et al.   BRITISH JOURNAL OF NUTRITION

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

(2012) Pablo Cingolani et al.   FLY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford 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

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Pea (Pisum sativum L.) in the Genomic Era

(2012) Petr Smýkal et al.   Agronomy-Basel

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Mendel’s Genes: Toward a Full Molecular Characterization: Table 1 

(2011) James B. Reid et al.   GENETICS

Crop genomics: advances and applications

(2011) Peter L. Morrell et al.   NATURE REVIEWS GENETICS

Mendel, 150 years on

(2011) T.H. Noel Ellis et al.   TRENDS IN PLANT SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nuclear genome size: Are we getting closer?

(2010) Jaroslav Doležel et al.   CYTOMETRY PART A

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Phylogeny, phylogeography and genetic diversity of the Pisum genus

(2010) Petr Smýkal et al.   Plant Genetic Resources-Characterization and Utilization

Identification of Mendel's White Flower Character

(2010) Roger P. Hellens et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Analysis of a diverse global Pisum sp. collection and comparison to a Chinese local P. sativum collection with microsatellite markers

(2008) Xuxiao Zong et al.   THEORETICAL AND APPLIED GENETICS