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Genomics In The Journals: Jan 19, 2012

NEW YORK (GenomeWeb News) – An international team led by investigators at the University of Melbourne and BG1-Shenzhen have sequenced the genome of the blood fluke Schistosoma haematobium, known for causing urogenital disease and boosting both bladder cancer and HIV susceptibility risk.

As they report in Nature Genetics, the researchers unraveled the fluke's 385,000 base genome using DNA from a male and female fluke pair. The researchers' genome and RNA-sequence data offered clues to the parasite's gene content, as well as gene interactions and expression patterns in flukes from different sexes and life cycle stages. Comparisons with S. mansoni and S. japonicum, fluke species that had their genomes sequenced previously, helped flesh out relationships between the flukes and pointed to possible genetic contributors to each fluke's preferred lifestyle.

"Unlocking the molecular biology of this and related disease pathogens of global importance will offer new insights into schistosome development, host-parasite affiliations, disease, and schistosomiasis-associated bladder cancer," University of Melbourne veterinary science researcher Robin Gasser, the study's co-corresponding author, and colleagues write, "and will underpin the design of new diagnostic tools, anti-schistosome drugs and vaccines."

Also in Nature Genetics, a look at how genetic and metabolic patterns can help predict the presence of complex traits in hybrid maize plants. German and Saudi Arabian researchers brought together SNP genotyping data and information on more than 100 metabolites for 285 diverse inbred lines and then looked at how these profiles corresponded to phenotypes in hybrid strains generated by crossing the inbred lines with test lines. In particular, they focused on seven traits with potential relevance for maize biomass or bioenergy in the hybrid maize lines, which were grown under half a dozen different environmental conditions.

"Whole-genome and metabolic prediction models were built by fitting effects for all SNPs or metabolites," University of Hohenheim researcher Albrecht Melchinger, the study's corresponding author, and colleagues explained, "allowing a reliable screening of large collections of diverse inbred lines for their potential to create superior hybrids."

In PLoS ONE, an international research team presents a corrected version of a 2010 longevity study that they published in Science but retracted last summer due to errors related to the microarray used in the research.

For the current version of the study, researchers did a genome-wide association study involving 801 individuals over the age of 100 years old from the New England Centenarian Study and 914 healthy controls from the same population. Based on findings from the discovery group, investigators developed a 281-SNP set for predicting longevity that they then tested in two more centenarian and control cohorts. The genetic signature predicted longevity with between 60 and 85 percent accuracy, they report. An additional genetic clustering analyses hinted at the potential presence of genetic sub-types within the centenarian group.

Meanwhile, researchers from Australia and the UK used a GWAS approach to begin looking at how genetics influences the maintenance of mental acuity over an individual's lifetime. The investigators genotyped samples from more than 1,900 individuals from Scottish birth cohorts who had taken standardized general intelligence tests when they were 11 years old for mental health surveys done in 1932 and 1947. Individuals took cognitive and other tests again when they were 65, 70, or 79 years old. Results from the study, published online in Nature, suggest genetic factors do contribute to changes in general intelligence as we age, though environmental factors seem to have a more pronounced effect.

"The results … strongly suggest how important the environment is helping us to stay sharp as we age," University of Queensland researcher Peter Visscher, co-corresponding author, said in a statement.

"Neither the specific genetic nor environmental factors were identified in this research," he added. "Our results provide the warrant for others and ourselves to search for those."

A University of Utah team used microsatellite genotyping to explore the genetic basis of the extensive variation found in pigeon breeds — work they outline in a Current Biology study. The researchers genotyped 360 pigeons representing 70 domestic breeds and two wild pigeon populations from Salt Lake City and Scotland. Based on their phylogenetic analyses using data at almost three-dozen microsatellite markers, the group was able to untangle relationships between the breeds and dig down to their geographic origins. The work also illustrates the processes contributing to the evolution of some pigeon traits, study authors say, opening the door for further study of the genes behind these traits.

"Most people think of pigeons as rats of the sky, but domestic pigeon breeds are wonderfully diverse," University of Utah biologist Michael Shapiro, the study's corresponding author, said in a statement.

"The striking differences we see between breeds within this single species are characteristic of the types of differences we typically see between species," he added. "Our hope is that by understanding the genes that control pigeon diversity, we'll have a great starting point to understand diversity in the wild."

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

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