Emerging Knowledge from Genome Sequencing of Crop Species

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

(2011) Eudald Illa et al.   BMC EVOLUTIONARY BIOLOGY

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

(2011) Minkyu Park et al.   BMC GENOMICS

Palaeogenomics in cereals: Modeling of ancestors for modern species improvement

(2011) Jérôme Salse et al.   COMPTES RENDUS BIOLOGIES

Molecular evolution of two duplicated CDPK genes CPK7 and CPK12 in grass species: A case study in wheat (Triticum aestivum L.)

(2011) Shuaifeng Geng et al.   GENE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Identification of EMS-Induced Causal Mutations in a Non-Reference Arabidopsis thaliana Accession by Whole Genome Sequencing

(2011) N. Uchida et al.   PLANT AND CELL PHYSIOLOGY

Journey through the past: 150 million years of plant genome evolution

(2011) Sebastian Proost et al.   PLANT JOURNAL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Next-Generation Sequencing Reveals Recent Horizontal Transfer of a DNA Transposon between Divergent Mosquitoes

(2011) Yupu Diao et al.   PLoS One

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast-forward genetics enabled by new sequencing technologies

(2011) Korbinian Schneeberger et al.   TRENDS IN PLANT SCIENCE

Insights from the Comparison of Plant Genome Sequences

(2010) Andrew H. Paterson et al.   Annual Review of Plant Biology

Genomic resources in horticultural crops: Status, utility and challenges

(2010) Humira Sonah et al.   BIOTECHNOLOGY ADVANCES

Molecular evolution of the duplicated TFIIAγ genes in Oryzeae and its relatives

(2010) Hong-Zheng Sun et al.   BMC EVOLUTIONARY BIOLOGY

Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)

(2010) Jianjun Xu et al.   BMC GENOMICS

SNP discovery by high-throughput sequencing in soybean

(2010) Xiaolei Wu et al.   BMC GENOMICS

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

(2010) Tim van Zutphen et al.   BMC GENOMICS

Grass genome organization and evolution

(2010) Katrien M Devos   CURRENT OPINION IN PLANT BIOLOGY

The Impact of Whole Genome Sequencing on Model System Genetics: Get Ready for the Ride

(2010) O. Hobert   GENETICS

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution

(2010) F. Murat et al.   GENOME RESEARCH

Getting domestication straight:ramosa1in maize

(2010) HANNES DEMPEWOLF   MOLECULAR ECOLOGY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology

(2010) Steven D. Rounsley et al.   PLANT JOURNAL

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

High throughput DNA sequencing: The new sequencing revolution

(2010) Michel Delseny et al.   PLANT SCIENCE

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

(2010) W. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Palaeogenomics of plants: synteny-based modelling of extinct ancestors

(2010) Michael Abrouk et al.   TRENDS IN PLANT SCIENCE

A triptych of the evolution of plant transposable elements

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

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

The Future of Rice Genomics: Sequencing the Collective Oryza Genome

(2010) Jose Luis Goicoechea et al.   Rice

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

Grapevine genetics after the genome sequence: Challenges and limitations

(2009) J.M. MARTÍNEZ-ZAPATER et al.   AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH

From DNA Sequence to Plant Phenotype: Bioinformatics Meets Crop Science

(2009) Primetta Faccioli et al.   Current Bioinformatics

Genomic and expression plasticity of polyploidy

(2009) Scott Jackson et al.   CURRENT OPINION IN PLANT BIOLOGY

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Impact of transposable elements on the organization and function of allopolyploid genomes

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

Structure and expression analysis of rice paleo duplications

(2009) M. Throude et al.   NUCLEIC ACIDS RESEARCH

Plant genome sequencing: applications for crop improvement

(2009) David Edwards et al.   PLANT BIOTECHNOLOGY JOURNAL

Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

(2009) S. Myles et al.   PLANT CELL

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

(2009) S. B. Cannon et al.   PLANT PHYSIOLOGY

High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology

(2009) Diana Rigola et al.   PLoS One

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

(2009) J. Salse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Palomero Genome Suggests Metal Effects on Domestication

(2009) J.-P. Vielle-Calzada et al.   SCIENCE

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

The give-and-take of DNA: horizontal gene transfer in plants

(2009) Ralph Bock   TRENDS IN PLANT SCIENCE

Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification

(2009) Kousuke Hanada et al.   PLoS Genetics

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

(2008) J. A. Reinhardt et al.   GENOME RESEARCH

Revisiting horizontal transfer of transposable elements in Drosophila

(2008) E L S Loreto et al.   HEREDITY

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

(2008) J. S.S. Ammiraju et al.   PLANT CELL

Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution

(2008) J. Salse et al.   PLANT CELL

Evolutionary and functional study of the CDPK gene family in wheat (Triticum aestivum L.)

(2008) Ai-Li Li et al.   PLANT MOLECULAR BIOLOGY

Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences

(2008) J.-M. Celton et al.   Tree Genetics & Genomes

Conserved themes in small-RNA-mediated transposon control

(2008) Angélique Girard et al.   TRENDS IN CELL BIOLOGY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources