Search

Phaeocystales are ecologically significant nanoplankton whose evolutionary history and functional diversity remain incompletely characterized. Here, the authors integrate genomic and transcriptomic data to reveal their lineage diversification, metabolic plasticity, and adaptation to polar and temperate regimes.

The haplotype-resolved genome in Amborella trichopoda addresses outstanding questions on the structure and gene content of the recently evolved ZW sex chromosomes.

The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.

In poplar, a quantitative genetic screen identifies a G-type lectin receptor-like kinase that mediates ectomycorrhizal symbiosis with Laccaria bicolor. Expression of the kinase in non-host Arabidopsis makes mycorrhizal colonization possible.

The genome of the model fern species Ceratopteris richardii reveals a history of remarkably dynamic genome evolution, including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago.

Genome assemblies of four filamentous Zygnematophyceae and co-expression network analyses shed light on the evolutionary roots of the mechanism for balancing environmental responses and multicellular growth.

Fungi from the Neocallimastigomycetes taxonomic class break bonds in lignin during the anaerobic deconstruction of whole plant cell walls. This finding challenges the paradigm that only certain aerobic organisms break down lignin.

This description of the Sphagnum (peat moss) genome includes a newly discovered sex chromosome. Interactions among sex, autosomes and environment show direct effects on Sphagnum growth which influences global carbon sequestration.

Genomes of three Tuberaceae species and two related truffle species reveal genetic similarities across symbiotic truffle-forming fungi, including high expression of genes involved in volatile organic compound metabolism.

Metabolism can influence gene expression through histone modifications. Using a mouse model of the inborn error of metabolism propionic acidaemia, Park et al. show how raised propionate levels produce epigenetic actions that impact cardiac function.

More than 400 parallel enrichment experiments from goat faeces are analysed using metagenomics to evaluate how substrate and antibiotic selection affect membership, activity, stability and chemical productivity of herbivore gut microbiomes.

Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

Newly sequenced seagrass genomes unveil a hexaploid ancestry for seagrasses. The transition to marine environments involved fine-tuning of many processes that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been rare.

Zymoseptoria tritici is an important fungal pathogen of wheat which has spread globally. Here, the authors perform genomic analyses on a collection of ~1100 Z. tritici samples from 42 countries to describe its global spread and elucidate mechanisms of adaptation to different environmental conditions.

Chromosomal inversions can promote speciation. Here, the authors identify a young inversion that has captured ecologically important genetic variants in a hybrid zone of the plant Boechera stricta, promoting local adaptation and incipient speciation.

The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

Existing examples of targeted gene insertion in plants either rely on a selectable marker gene or result in short DNA inserts. Here, the authors use an optimized CRISPR-Cas9 method to insert a 5.2 kb carotenoid biosynthesis cassette into genomic safe harbors in rice, and obtain marker-free lines with high carotenoid content.

Sequencing the nuclear genomes of Guillardia theta and Bigelowiella natans, transitional forms in the endosymbiotic acquisition of photosynthesis by engulfment of certain eukaryotic algae, reveals unprecedented alternative splicing for a single-celled organism (B. natans) and extensive genetic and biochemical mosaicism, shedding light on why nucleomorphs persist in these species but not other algae.

The ascomycete Cenococcum geophilum is a beneficial mycorrhizal symbiont found frequently on tree roots. Here the authors use comparative genomics and transcriptomics to define genomic signatures that differentiate the beneficial C. geophilumfrom its saprotrophic and pathogenic relatives.

Existing plant pan-genomic studies usually report considerable intraspecific whole gene presence-absence variation. Here, the authors use pan-genomic approach to reveal gradual polyploid genome evolution by analyzing of Brachypodium hybridum and its diploid progenitors.

De novo assembly of 23 Aspergillus section Nigri and 6 Aspergillus niger genome sequences allows for inter- and intraspecies comparisons and prediction of secondary metabolite gene clusters.

Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify genetic determinants of endophytism.

Aspergillus fungi classified within the section Flavi include harmful and beneficial species. Here, Kjærbølling et al. analyse the genomes of 23 Flavi species, showing high genetic diversity and potential for synthesis of over 13,700 CAZymes and 1600 secondary metabolites.

A phylogenetic tree of 5,284 fungal species is used to infer patterns of extinction, diversification and morphological innovation in mushroom-forming fungi.

The fungal genus Armillaria includes virulent necrotrophic pathogens, unusual wood decayers and the largest terrestrial organisms on Earth. Sahu et al. suggest that horizontal gene transfer contributed to the evolution of some of these unique traits.

Paspalum vaginatum is a stress tolerant wild relative of maize and sorghum. Here, the authors assemble its genome at pseudomolecule level and reveal the role of trehalose mediated autophagy in increasing maize biomass productivity under nutrient-deficit conditions.

Soybean is an important crop plant, providing seed protein and oil and fixing atmospheric nitrogen through symbioses with soil-borne microorganisms. Using a whole-genome shotgun approach, its 1.1-gigabase genome is now sequenced and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly.

Completion of genome sequences for the diploid Setaria italica reveals features of C₄ photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass (Panicum virgatum). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted.

Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications.

Fungi of the genus Armillaria include devastating forest pathogens that cause root rot disease in many plants. Sequencing genomes and transcriptomes of several species, the authors reveal the genetic basis of dispersal, multicellular development and pathogenic mechanisms in Armillaria.

Drought is a major factor limiting crop productivity. Here, via eQTL analysis and comparative genomics, the authors show compensatory evolution between trans-regulatory loci and transcription factor binding sites that shape the drought response networks in the model C4 grass Panicum hallii.

The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression.

The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.

Polar microalgae have high zinc demand. Here, the authors use quantitative proteomics and transcriptomics of polar and non-polar model algae combined with cellular physiology to show that zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton.

Wood-feeding 'higher' termites rely on their hindgut symbionts for the intitial steps in cellulose degradation. Metagenomic analysis of this microbial community reveals a diverse range of bacterial cellulase and hydrolase genes, as well as genes important in other metabolic functions, such as H2 metabolism, CO₂-reductive acetogenesis and N₂ fixation.

The genome of the wild grass Brachypodium distachyon (Brachypodium), a member of the Pooideae subfamily, is sequenced. The Pooideae are one of three subfamilies of grasses that provide the bulk of human nutrition and may become major sources of renewable energy. Availability of the genome sequence should help establish Brachypodium as a model for developing new energy and food crops.

The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from the genomes of its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness.

This study identifies the proteins critical to fungal cellulosome assembly, characterizing the complex as evolutionarily chimeric — an independently evolved fungal complex co-opted catalytic activities from bacteria coexisting within the gut.

Sequencing wild relatives of millet identifies genes that regulate yield and harvesting traits.

Francis Martin and colleagues report genome sequences for 18 species of mycorrhizal fungi and a phylogenomic analysis including 32 other fungal genomes. The study identifies cell wall-degradation genes lost in all true ectomycorrhizal species and, using gene expression data, finds candidate genes for the establishment of symbiosis.

Analysis of the virus community associated with red algal mats in Yellowstone National Park shows it to be dominated by Megaviricetes, with resident virus lineages being of ancient origin and encoding genomic footprints of adaptation to thermophily.

The authors analyzed the response of an Arctic pelagophyte to lowered salinity. They observed that several ancient and widespread pathways were activated, allowing the species to adjust to the stress of rapid salinity change.

Arctic microalgae show specific adaptation to cold saline arctic conditions with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation.