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January 11, 2018

All in the Family: Focused Genomic Comparisons

Colonies of Aspergillus: A. campestris; A. ochraceoroseus; and, A.steynii. These 3 species were among those whose genomes were sequenced in the study. (Kirstine Ellen Lyhne, DTU)Genus-wide Aspergillus project highlights new functional genome annotation methods. Found in microbial communities around the world, Aspergillus fungi are pathogens, decomposers, and important sources of biotechnologically-important enzymes. Each Aspergillus species is known to contain more than 250 carbohydrate active enzymes (CAzymes), which break down plant cell walls and are of interest to Department of Energy… [Read More]

January 8, 2018

The fungus that made itself at home

Serpula lacrymans var shastensis decomposing a large Shasta red fir (Abies magnifica var shastenis) in its natural habitat in Mt Shasta, California. (Håvard Kauserud)Retracing how the dry rot Serpula lacrymans adapted to a new ecological habitat. The Science By comparing genetic information from similar organisms, researchers have gained insights on why the dry rot (Serpula lacrymans) is so destructive in houses. A study involving six brown rot fungi reveals the genomic changes Serpula lacrymans has undergone in adapting… [Read More]

December 20, 2017

When One Reference Genome is Not Enough

A single reference genome is not enough to harness the full genetic variation of a species so pan-genomes of crops would be extremely useful. The phenotypic diversity of Brachypodium plants is shown here. (John Vogel)Much of the research in the field of plant functional genomics to date has relied on approaches based on single reference genomes. But by itself, a single reference genome does not capture the full genetic variability of a species. A pan-genome, the non-redundant union of all the sets of genes found in individuals of a… [Read More]

December 18, 2017

A Functional Genomics Database for Plant Microbiome Studies

Phylogenetic tree of 3,837 high quality and non-redundant bacterial genomes. Outer ring denotes the taxonomic group, central ring denotes the isolation source, and inner ring denotes the root-associated genomes within plant-associated genomes. Taxon names are color-coded based on phylum: green – Proteobacteria, red – Firmicutes, blue – Bacteroidetes, purple - Actinobacteria. (Asaf Levy)Catalog of candidate genes involved in plant-microbe relationships. As the global population rises, estimated to hit nearly 10 billion by 2050, so does the need to boost crop yields and produce enough plant material for both food and sustainable alternative fuels. To help improve crop breeding strategies and overcome challenges such as making plants more… [Read More]

December 16, 2017

Colleen Hansel, Woods Hole Oceanographic Institute

Colleen Hansel, fungal collaborator at WHOIHow long have you collaborated with JGI?  I started collaborating with JGI in the Fall of 2013 as part of a Facilities Integrating Collaborations for User Science (FICUS) award between JGI and the Environmental Molecular Sciences Laboratory (EMSL). (Click here to learn more about her approved FICUS proposal.) We have been working with the JGI… [Read More]

December 13, 2017

An Addiction Crucial to a Fungus’ Reproduction

Sexual reproduction in Rhizopus microspores: (a) Successful mating between fungi harboring bacteria; (b) Lack of sex between mates cured of endobacteria. (Stephen Mondo)A fungus relies on bacteria to regulate key components of its reproductive machinery The Science To better understand how beneficial organisms (symbionts) are transmitted between host generations, researchers investigated the role that bacteria living within a host (endosymbionts) have on fungal host reproduction, and the reproductive genes they regulate. The bacterial endosymbiont, Burkholderia, is recognized… [Read More]

December 1, 2017

Succulent Genes for Water Use Efficiency

In Nature Communications, researchers sequenced and analyzed the genome of Kalanchoe fedtschenkoi (lavender scallops) to better understand how this plant transitioned from C3 to CAM photosynthesis. (Forest and Kim Starr, Flickr CC BY 2.0)Comparative genomics identifies sequences involved in photosynthesis under reduced water conditions.   The Science In the presence of sufficient water and light, most plants conduct photosynthesis through what is known as the C3 pathway. As plants spread out and adapted to live in a variety of environments, they developed alternate photosynthesis pathways, known as C4 and… [Read More]

November 24, 2017

Insights into carbon fixation in the dark ocean  

View of Saanich Inlet - one of the areas sampled for this study - from Malahat. (BC Ministry of Transportation, Flickr CC BY-NC-ND 2.0)Nitrite-oxidizing bacteria have bigger role in marine carbon cycle than previously thought The Science Researchers have identified the most abundant and globally distributed nitrite-oxidizing bacteria (NOB) in the oceans, through single-cell genomics and community meta-omics. They have also calculated the NOB’s contribution toward trapping carbon beneath the sunlit waters and determined that though these bacteria… [Read More]

November 16, 2017

J. Chris Pires, University of Missouri

J. Chris Pires, University of Missouri“JGI has phenomenal scientists and staff who are part of our dream team.”   How long have you collaborated with the JGI? I have been involved with the JGI Community Science Program (CSP) since 2012. I am involved in two JGI projects. The first one is the Brassicales Map Alignment Project (BMAP), which was funded… [Read More]

October 30, 2017

White Rot Fungi’s Size Explained by Breadth of Gene Families Involved

Clusters of fruiting bodies emerge on and around trees in Armillaria-infected areas in the fall. (Virág Tomity)Comparative genomics involving humongous fungus helps explain evolution of Armillaria Among the contenders for the world’s largest living organism is something usually considered much smaller than a blue whale, or a towering sequoia. This particular organism is so big, one needs an aerial map to grasp its size, and even then it’s not completely visible… [Read More]
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