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Genomics In The Journals: Jun 16, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A team of researchers from the US Department of Energy's Joint Genome Institute, Plant Research International in the Netherlands, and elsewhere report on the finished genome of Mycosphaerella graminicola, a fungus that causes leaf blotch in wheat, in PLoS Genetics. Comparisons between the fungus' 39.7 million base genome and sequences from other fungi suggest M. graminicola lacks many enzymes that other fungal pathogens use to attack plant cell walls — a feature that the researchers suspect may help it hide from its host plant.

"The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection," the study authors wrote, "and may have evolved from endophytic ancestors."

An international research group published a study in Nature Genetics describing how it found three genetic loci that ramp up the risk of migraines. The researchers found seven suspicious loci through a population-based, genome-wide association study involving 5,122 women of European ancestry who suffer from migraines and were enrolled through the Women's Genome Health Study and 18,108 unaffected women from the same population. They subsequently linked three of these — SNPs on chromosomes 1, 2, and 12 that fall in and around the PRDM16, TRPM8, and LRP1 genes — to migraine risk through meta-analyses involving three more European cohorts, along with analyses of individuals from both the discovery and replication groups.

The giant Mimivirus can lose large chunks of its genome when grown in the absence of other microbes typically sharing a community with it inside amoebas, according to a new study in the Proceedings of the National Academy of Sciences. Senior author Didier Raoult, a Université de la Méditerranée infectious and tropical disease researcher who led a team that sequenced the Mimivirus genome in 2009, and his co-workers found that the virus loses roughly 17 percent of its genome size — going from 1.2 million bases to 993,000 bases — when cultured for 150 passages in germ-free amoeba hosts.

"Overall, the Mimivirus transition from a sympatric to an allopatric lifestyle was associated with a stepwise genome reduction and the production of a predominantly bald virophage resistant strain," Raoult and colleagues wrote. "The new axenic ecosystem allowed the allopatric Mimivirus to lose unnecessary genes that might be involved in the control of competitors."

In another early, online PNAS study, Brown University researchers make the case for expanding the view of messenger RNA splicing errors in disease, suggesting such errors may be more common in risk allele databases than previously appreciated. The team took a computational approach to looking at relationships between splicing element locations in the genome, sequence variation, and functional information. Together, their findings hint that past studies may have under-estimated the proportion of disease-related alleles that actually alter mRNA splicing.

"Analyzing the dataset of human disease … suggested that 22 percent of disease alleles that were originally classified as missense mutations may also affect splicing," senior author William Fairbrother, a computational molecular biology, genomics, and proteomics researcher at Brown, and co-authors wrote. "This category together with mutations in the canonical splicing signals suggest that approximately one third of all disease-causing mutations alter pre-mRNA splicing."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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