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Genomics of Energy and Environment

Purdue University's Jody Banks kicked off the scientific sessions at the US Department of Energy Joint Genome Institute's 7th annual User Meeting in Walnut Creek, Calif., this week with her talk on the Selaginella genome and how sequencing diverse species could help researchers understand plant evolution. The Selaginella genome — though small, at around 100 million basepairs — is the first fully sequenced lycophyte, and could hold important insights as to the evolution of lignin, Banks said. During her talk, Banks also made a case for sequencing fern genomes.

Fred Gmitter at the University of Florida spoke about how the 'omics are being applied to improve citrus breeding, particularly in regards to disease resistance. Gmitter discussed about how the insect-vectored, phloem-limiting bacterium Candidatus Liberibacter-based citrus greening disease has diminished global production.

Clark University's David Hibbett discussed "how mushrooms changed the world" and charted the ecological evolution of white rot and brown rot fungi. During his talk, Hibbett referenced JGI's 1,000 Fungal Genomes Project, saying that it could help transform mycology into a genome-driven science.

Later, Robert Goldberg at the University of California, Los Angeles, spoke of using various 'omics approaches to understand seed development in soybean. Goldberg talked about his group's efforts to analyze the transcriptome and methylome of the entire seed, as well as its distinct parts, throughout development, among other things.

During his talk, Loren Rieseberg at the University of British Columbia noted the many technical challenges surrounding sequencing the sunflower genome. While its size is a considerable issue, the biggest problem when it comes to sequencing the sunflower genome is that many of its long terminal repeats are young, he said.

In the afternoon, Eske Willerslev at the University of Copenhagen discussed sequencing and analyzing ancient human genomes, and introduced a variety of ongoing projects in his lab — from the genome of Sitting Bull to a study on horse evolution and domestication. Then, Lawrence Berkeley National Laboratory's Adam Arkin introduced the DOE Systems Biology Knowledgebase, or Kbase. The resource, which is currently in development and scheduled for a February 2013 production release, aims to foster interactive knowledge and drive "data toward dynamic models of function."

Also, Shawn Kaeppler at the University of Wisconsin-Madison talked about his group's genomic analysis of variation in maize seed and plant size, while Cold Spring Harbor Laboratory's Michael Schatz closed out the day's talks with a discussion of interpretation in "the era of mega-genomics." Even with access to infinite samples and experiments, Schatz said, analyses are "ultimately limited by human capacity to execute extremely complex experiments and interpret results."

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.