The Earth BioGenome project: opportunities and challenges for plant genomics and conservation

Genomes of skipper butterflies reveal extensive convergence of wing patterns

(2019) Wenlin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early Sex-chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua

(2019) Paris Veltsos et al.   GENETICS

Advances and Applications in the Quest for Orthologs

(2019) Natasha Glover et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global tree restoration potential

(2019) Jean-Francois Bastin et al.   SCIENCE

Global dataset shows geography and life form predict modern plant extinction and rediscovery

(2019) Aelys M. Humphreys et al.   Nature Ecology & Evolution

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Adaptive introgression: a plant perspective

(2018) Adriana Suarez-Gonzalez et al.   Biology Letters

Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion

(2018) Paul Jay et al.   CURRENT BIOLOGY

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics of the nonlegumeParasponiareveals insights into evolution of nitrogen-fixing rhizobium symbioses

(2018) Robin van Velzen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

10KP: A phylodiverse genome sequencing plan

(2018) Shifeng Cheng et al.   GigaScience

Using herbaria to study global environmental change

(2018) Patricia L. M. Lang et al.   NEW PHYTOLOGIST

Domestication of wild tomato is accelerated by genome editing

(2018) Tingdong Li et al.   NATURE BIOTECHNOLOGY

De novo domestication of wild tomato using genome editing

(2018) Agustin Zsögön et al.   NATURE BIOTECHNOLOGY

New Approaches for Genome Assembly and Scaffolding

(2018) Edward S. Rice et al.   Annual Review of Animal Biosciences

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

(2017) Wen-Biao Jiao et al.   GENOME RESEARCH

New advances in sequence assembly

(2017) Adam M. Phillippy   GENOME RESEARCH

Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)

(2017) Christian R. Voolstra et al.   INVERTEBRATE SYSTEMATICS

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

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

The Fate of the World’s Plants

(2017) Stuart L. Pimm et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

(2017) Moises Exposito-Alonso et al.   Nature Ecology & Evolution

Pathways to de-extinction: how close can we get to resurrection of an extinct species?

(2016) Beth Shapiro   FUNCTIONAL ECOLOGY

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

Borrowed alleles and convergence in serpentine adaptation

(2016) Brian J. Arnold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Climate-Related Local Extinctions Are Already Widespread among Plant and Animal Species

(2016) John J. Wiens   PLOS BIOLOGY

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Time to get moving: assisted gene flow of forest trees

(2015) Sally N. Aitken et al.   Evolutionary Applications

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis

(2014) Maharaj K. Pandit et al.   NEW PHYTOLOGIST

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

The biodiversity of species and their rates of extinction, distribution, and protection

(2014) S. L. Pimm et al.   SCIENCE

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes

(2012) Aline Muyle et al.   PLOS BIOLOGY

Sex Chromosomes in Land Plants

(2011) Ray Ming et al.   Annual Review of Plant Biology

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

(2011) Tina T Hu et al.   NATURE GENETICS

The largest eukaryotic genome of them all?

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

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand

(2009) Simon Joly et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

(2008) Ary A. Hoffmann et al.   Annual Review of Ecology Evolution and Systematics

Global change and species interactions in terrestrial ecosystems

(2008) Jason M. Tylianakis et al.   ECOLOGY LETTERS

Environmental change and the option value of genetic diversity

(2008) Alistair S. Jump et al.   TRENDS IN PLANT SCIENCE

Low X/Y divergence in four pairs of papaya sex-linked genes

(2007) Qingyi Yu et al.   PLANT JOURNAL