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Genomics In The Journals: Aug 9, 2012

NEW YORK (GenomeWeb News) – An international team led by investigators at the Wellcome Trust Sanger Institute delves into the genetics and evolutionary history of a dysentery-causing microbe called Shigella sonnei that has become more widespread in rapidly industrializing regions, including places with improved water quality. This pattern opposes that established for the related species called S. flexneri, a frequent dysentery culprit in developing countries which tends to wane once clean water sources are available.

As they report in Nature Genetics, the researchers sequenced the genomes of 132 S. sonnei isolates collected on four continents over more than six decades. By comparing these sequences to one another and looking at the relationships between isolates from different locales, the team determined that the forms of S. sonnei that are currently circulating stem from an ancestral strain that diversified in Europe within the last 500 years. From there, it appears to have spawned three related lineages that spread to other parts of the world, fueled in part by genetic adaptations that have given the bugs the ability to resist a wide range of antibiotic treatments.

"The two most recent lineages have been continually evolving to become increasingly resistant to antimicrobials," study co-author Stephen Baker, a researcher with Oxford University's clinical research unit in Vietnam, explained in a statement. "Our data is consistent with antibiotic resistance as being a main driver of the spread and persistence of S. sonnei around the world, stressing that antibiotics are not a long-term solution for the elimination of this global health problem."

In another Nature Genetics study, researchers from Germany and elsewhere report on new risk loci for nonsyndromic cleft lip, a condition characterized by incomplete lip development that's sometimes accompanied by additional malformations affecting the roof of the mouth, known as cleft palate.

For its meta-analysis, the team looked at data for nearly 2,000 individuals of European or Asian descent with nonsyndromic cleft lip (with or without cleft palate) who had been assessed through two previous genome-wide association studies. For almost 1,500 of the cases, the investigators also had access to genotyping data on the affected individuals' parents. In addition to finding a handful of known risk loci for cleft lip, the researchers narrowed in on new cleft lip-associated SNPs at half a dozen sites in the genome. Five of the loci appear to contribute to cleft lip risk in both European and Asian populations. Among them: a chromosome 13 locus that seems to be especially associated with cases involving both cleft and cleft palate. A sixth cleft lip risk locus, on chromosome 15, only reached genome-wide significance in the European samples.

Two papers in the Proceedings of the National Academy of Sciences online look at the particulars of sex chromosome evolution in the papaya plant. The plant's two Y chromosomes — one involved in sexual reproduction and another found in hermaphroditic papaya plants — and its female X chromosome are believed to have evolved relatively recently, around seven million years ago.

For each of the studies, research teams from the US and UK relied on existing papaya genome and RNA sequence data as well as new, targeted sequence information generated for the papaya and/or a related plant species. Together, the analyses suggest that the papaya sex chromosomes have been taking on new repetitive elements that are making them larger. At the same time, the sex chromosomes seem to be shuffling their genetic repertoires through chromosomal rearrangement and losing genes that used to serve autosomal chromosome functions. This pattern is not exclusive to the Y chromosome, researchers found, but appears to be occurring on the X chromosome as well, albeit at a slower rate.

"These studies are changing our view of sex chromosome evolution, particularly X chromosome evolution," University of Illinois at Urbana-Champaign plant biology researcher Ray Ming, senior author on both studies, said in a statement. "We now know that both the X and Y chromosomes are dynamic in the early stages of their evolution, not only the Y chromosome, as previously thought."

In an American Journal of Human Genetics study, researchers from Stanford University, the HudsonAlpha Institute for Biotechnology, and the University of Michigan take a closer look at homozygosity patterns in human populations.

Using information at almost 580,000 autosomal SNPs in 1,839 individuals from dozens of human populations, the team tracked runs of homozygosity that they classified as short, intermediate, or long. The number and size of these sequences varied from one individual to the next, they found, though the overall patterns point to runs of homozygosity in the short and intermediate ranges that stretch out in populations found further and further from East Africa. Long runs of homozygosity varied more dramatically between individuals, but turned up more often in populations that allow or encourage marriages between related individuals. The team also explored some of the genomic features associated with homozygous sequences, uncovering patterns that are expected to inform future studies of everything from human evolutionary history and genetic variation to disease risk.

"These results provide insight into the way in which homozygosity patterns are produced," Stanford University biologist Trevor Pemberton, the study's corresponding author, and his colleagues wrote, "and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive disorders."

The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.