Why size really matters when sequencing plant genomes

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Exploring giant plant genomes with next-generation sequencing technology

(2011) Laura J. Kelly et al.   CHROMOSOME RESEARCH

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

(2011) S. Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Space Dynamics During the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

(2011) A. N. Massa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Dynamo maker ready to roll

(2011) Susan Young   NATURE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Sequencing crop genomes: approaches and applications

(2011) Scott A. Jackson et al.   NEW PHYTOLOGIST

Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives

(2011) Thomas Wicker et al.   PLANT CELL

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

(2011) Pilar Hernandez et al.   PLANT JOURNAL

Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes

(2011) Roger Barthelson et al.   PLoS One

Green Genomes

(2011) E. Pennisi   SCIENCE

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

(2010) Kateřina Ambrožová et al.   ANNALS OF BOTANY

Assembling the Angiosperm Tree of Life: Progress and Future Prospects

(2010) Douglas E. Soltis et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Insights from the Comparison of Plant Genome Sequences

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

Structural variation analysis with strobe reads

(2010) A. Ritz et al.   BIOINFORMATICS

Unfurling Fern Biology in the Genomics Age

(2010) Michael S. Barker et al.   BIOSCIENCE

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Patching gaps in plant genomes results in gene movement and erosion of colinearity

(2010) T. Wicker et al.   GENOME RESEARCH

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

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

(2010) Jinsheng Lai et al.   NATURE GENETICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

Genome Structures and Halophyte-Specific Gene Expression of the Extremophile Thellungiella parvula in Comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis

(2010) D.-H. Oh et al.   PLANT PHYSIOLOGY

Crop genome sequencing: lessons and rationales

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

Genome size diversity in orchids: consequences and evolution

(2009) I. J. Leitch et al.   ANNALS OF BOTANY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley

(2009) Thomas Wicker et al.   PLANT JOURNAL

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

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

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

(2009) Eduard Kejnovsky et al.   TRENDS IN ECOLOGY & EVOLUTION

A Single Molecule Scaffold for the Maize Genome

(2009) Shiguo Zhou et al.   PLoS Genetics

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae

(2008) M. A. Lysak et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring plant biodiversity: the Physcomitrella genome and beyond

(2008) Daniel Lang et al.   TRENDS IN PLANT SCIENCE

The Amborella genome: an evolutionary reference for plant biology

(2008) Douglas E Soltis et al.   GENOME BIOLOGY