Evolution by gene loss

R Albalat, C Cañestro - Nature Reviews Genetics, 2016 - nature.com
The recent increase in genomic data is revealing an unexpected perspective of gene loss as
a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This …

Orthologs, paralogs, and evolutionary genomics

EV Koonin - Annu. Rev. Genet., 2005 - annualreviews.org
Orthologs and paralogs are two fundamentally different types of homologous genes that
evolved, respectively, by vertical descent from a single ancestral gene and by duplication …

Insights into land plant evolution garnered from the Marchantia polymorpha genome

JL Bowman, T Kohchi, KT Yamato, J Jenkins, S Shu… - Cell, 2017 - cell.com
The evolution of land flora transformed the terrestrial environment. Land plants evolved from
an ancestral charophycean alga from which they inherited developmental, biochemical, and …

Phytozome: a comparative platform for green plant genomics

DM Goodstein, S Shu, R Howson… - Nucleic acids …, 2012 - academic.oup.com
The number of sequenced plant genomes and associated genomic resources is growing
rapidly with the advent of both an increased focus on plant genomics from funding agencies …

MycoCosm portal: gearing up for 1000 fungal genomes

IV Grigoriev, R Nikitin, S Haridas, A Kuo… - Nucleic acids …, 2014 - academic.oup.com
MycoCosm is a fungal genomics portal (http://jgi. doe. gov/fungi), developed by the US
Department of Energy Joint Genome Institute to support integration, analysis and …

The Ecoresponsive Genome of Daphnia pulex

JK Colbourne, ME Pfrender, D Gilbert, WK Thomas… - Science, 2011 - science.org
We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200
megabases and contains at least 30,907 genes. The high gene count is a consequence of …

The energetics of genome complexity

N Lane, W Martin - Nature, 2010 - nature.com
All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from
prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to …

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

WC Nierman, A Pain, MJ Anderson, JR Wortman… - Nature, 2005 - nature.com
Aspergillus fumigatus is exceptional among microorganisms in being both a primary and
opportunistic pathogen as well as a major allergen,,. Its conidia production is prolific, and so …

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

R Riley, AA Salamov, DW Brown… - Proceedings of the …, 2014 - National Acad Sciences
Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most
wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying …

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

D Martinez, RM Berka, B Henrissat, M Saloheimo… - Nature …, 2008 - nature.com
Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to
depolymerize biomass to simple sugars that are converted to chemical intermediates and …