Friday, March 1, 2013

DOE JGI Science Highlights: Sinking SOS levels lead to reduced salt tolerance

The Food and Agriculture Organization reported that salt levels in the soil is reducing the world’s agricultural lands at the rate of one percent a year. Concerns over feeding a growing global population with limited arable land have led to interest in developing salt-tolerant crops for food and fuel. 



Unlike its relative A. thaliana, (above) saltwater cress thrives 
in the presence of high salt levels. (Wikimedia Commons)

Friday, February 22, 2013

DOE JGI Science Highlights: Metagenomic study of methane in marine microbial communities

Methane is one of the most potent greenhouse gases and previous studies suggested that it is removed from the atmosphere through aerobic and anaerobic processes with the help of bacteria and archaea. Recent evidence suggests, however, that methane can be removed through other pathways involving as-yet unidentified microbes. 

lake washington and mount rainier by sethstoll, on Flickr
The study focused on samples of microbial communities active in methane oxidation
collected from Lake Washington.  
Creative Commons Attribution-Share Alike 2.0 Generic License by  sethstoll 

Friday, February 15, 2013

DOE JGI Science Highlights: Genome evolution with the help of plasmid gene pools


Plasmids are DNA molecules that can replicate independently of chromosomal DNA in a cell. This ability allows them to "collect" and move genes, such as through lateral gene transfer, and is a factor that allows prokaryotic genomes to evolve over time.

To understand the depth and breadth of this plasmid gene pool in prokaryotes, researchers including a team of DOE Joint Genome Institute researchers isolated, sequenced and compared plasmids from two activated wastewater sludge communities. In their report published February 14, 2013 in The ISME Journal, they noted the work done allowed them to study the “mobilome” or totality of mobile elements in a genome.



Sludge is collected at the bottom of settling tanks at
a wastewater treatment plant
. (Wikimedia Commons)

Friday, February 8, 2013

DOE JGI Science Highlights: Student tools for hands-on genomics and bioinformatics lessons

Driven in part by the increased emphasis to give life sciences students hands-on experience in “real research,” the DOE Joint Genome Institute’sGenomics and Bioinformatics Education Program developed a series of educational modules for undergraduate programs to explore and annotate publicly available microbial genome datasets. 



Overview of the IMG-ACT program structure. 
(Image from Ditty et al. Plos Biol. 2010; 8(8): e1000448. doi:10.1371/journal.pbio.1000448)
Known collectively as the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT), this bioinformatics interface is currently being used at more than 126 colleges and universities by 250 instructors and more than 5,600 students.

Friday, January 25, 2013

DOE JGI Science Highlights: Lessons learned from comparing Cochliobolus fungi

Cochliobolus fungi are cereal grain pathogens in the Dothideomycetes class, and many species are known to infect crops such as corn, rice, barley, wheat and oats, causing severe losses at harvest time and to biomass feedstocks for biofuels.


DSC_2695 by IRRI Images, on Flickr
Brown spot caused by a Cochliobolus fungal plant pathogen. 

In a study published January 24, 2013 in Plos Genetics, one in a series of publications concerning Dothideomycete fungi, DOE Joint Genome Institute collaborators Shaobin Zhong and Gillian Turgeon led a comparative genomic analysis of five Cochliobolus fungi--

Friday, January 11, 2013

DOE JGI Science Highlights: A fungal pathogen with a "genetically flexible" genome


In 2012, the damp winter threatened the wheat harvest in the state of Kansas, the nation’s single largest producer of the grain and wheat prices rose by 10 percent as a result.
Diseases such as tan spot caused by the fungus Pyrenophora tritici-repentis (Ptr) factored into the reduced wheat harvests. In North Dakota, which ranks second after Kansas in wheat production, tan spot and other diseases can reduce the crop by 10-15 percent annually. To get an idea of the economic impact of this loss, in 2010, the direct cash value of the state’s wheat crop was $2.2 billion, and generated an additional $4.5 billion in indirect commercial activity.

Tan spot on wheat by CIMMYT, on Flickr
Creative Commons Attribution-Noncommercial-Share Alike 2.0 Generic License by  CIMMYT 

Friday, January 4, 2013

DOE JGI Science Highlight: Benefits of “diversity-driven genome sequencing” in CyanoGEBA

Despite their miniscule size, cyanobacteria play significant roles in the global carbon and nitrogen cycles. Researchers are also looking at utilizing them for biofuel and biotechnology applications.

In an effort to learn more about the diverse strains in this phylum, DOE Joint Genome Institute scientist Cheryl Kerfeld is leading an effort called CyanoGEBA to increase the number of available cyanobacterial genomes for study. The project’s name is a nod to the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project that pioneered sequencinggenomes from under-represented branches in the Tree of Life

Cyanobacteria by Argonne National Laboratory, on Flickr
Chains of cyanobacteria. (Image courtesy of James Golden, UC San Diego)



Friday, December 21, 2012

DOE JGI Science Highlights: A Gossypium genome to cotton on to cellulose biosynthesis

Growing, processing and manufacturing cotton is a major global industry. In the United States, more than 200,000 domestic jobs are related to cotton production and processing, with an aggregate influence of about $35 billion on the annual U.S. gross domestic product. The fibers that have woven themselves into so many lives, however, are seen by bioenergy researchers as merely dozens of cellulose coils. These coils are of interest because cellulose is a target biomass for making biofuels.


Dozens of cellulose coils make up the fiber strands in this cotton boll. 
(Kathleen Phillips, Texas A&M AgriLife Research)

Cotton genome project in AL.com

If researchers' plans spin out as they hope, King Cotton may get a new title as a Super Plant of the 21st century.... While most U.S. cotton is used in textile production, researchers say it could become an important part of biofuel production and bioremediation.  

Full story at AL.com 

Friday, December 14, 2012

DOE JGI Science Highlights: Lifestyles of a fungal plant pathogen family

The fungi that belong to the Dothideomycetes family are found on every continent and can tolerate a wide range of environmental extremes. Additionally, several of the fungi are plant pathogens that infect nearly every major crop used for food, fiber or fuel.

In the December 6, 2012 issue of PLoS Pathogens, an international team led by researchers at the DOE Joint Genome Institute compared the genomes of 18 members of the Dothideomycetes family, 14 of which had been sequenced during the project. This work ties 
into a larger Community Sequencing Program project to sequence several Dothideomycete fungal species. It is also the main paper of a set on this fungal group, one of which was published November 29, 2012 in PLoS Genetics.


A fungal pathogen (C. sativus) from the Dothideomycetes family can cause 
severe economic losses to barley, a potential biofuels feedstock. 
(Shaobin Zhong, North Dakota State University)