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Genomics in the Journals: Jun 13, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, an international team led by investigators in Germany and Canada described findings from its genome sequencing study of Capsella rubella, a self-fertilizing plant from the same family as the well-characterized model organism Arabidopsis thaliana.

Using shotgun sequencing on genomic DNA from an Italian C. rubella line known as Monte Gargano, the researchers generated and assembled sequences spanning almost 135 million bases of the C. rubella genome sequence at an average depth of 22-fold. The assembly housed 26,521 predicted protein-coding genes, they found, along with almost 28,500 transcripts.

By adding in transcript sequences from for C. rubella and C. grandiflora (an out-crossing plant believed to represent the C. rubella progenitor plant), the team found variants and expression patterns that coincide with the transition to self-fertilization. Purifying selection appeared to be pronounced within Capsella species, study authors noted, as were changes to the plants' genome structure and transposable element repertoires.

"The factors driving … contrasting modes of genome expansion and shrinkage are far from resolved," co-corresponding authors Detlef Weigel, with the Max Planck Institute for Developmental Biology, and the University of Toronto's Stephen Wright, and colleagues concluded, "and it will be important to broaden future comparisons to larger phylogenetic scales to better understand the processes driving genome structure evolution."

A Journal of Dental Research study by researchers in the US and the UK looked at the possibility of using genetic profiles to predict — and potentially prevent — a form of gum disease called periodontitis.

In addition to analyses designed to unravel potential relationships between diabetes and/or smoking status and oral health, the researchers also used genotyping to look at a potential genetic contributor to periodontitis risk and tooth loss. For the latter experiments, they focused on a key variant within the immune gene interleukin-1, or IL-1, that was previously implicated in periodontitis.

The team, which included representatives from the Waltham, Mass.-based firm Interleukin Genetics, assessed mouth swab samples from nearly 5,300 individuals for whom tooth extraction insurance claim and questionnaire data were available. The presence or absence of the IL-1 variant of interest was determined by testing at Interleukin's CLIA-certified lab.

Investigators found the suspicious IL-1 variant in almost one-third of the 5,117 individuals successfully genotyped in the study. Their analysis indicated that those individuals were more prone to periodontitis and associated tooth loss over the 16 years for which dental records were available, hinting that IL-1 variant status might help in classifying individuals who would benefit from more vigilant preventative visits to the dentist.

Preferential paternal gene expression tends to outweigh preferential maternal expression amongst genes in placental tissue that have a parent-of-origin expression bias, a Proceedings of the National Academy of Sciences study suggests. Researchers from Cornell University did RNA sequencing on trophoblast tissue samples from the placentas of horses, donkeys, and mule or hinny hybrids (the offspring of crosses between male donkeys and female horses or male horses and female donkeys, respectively).

The analysis uncovered almost 80 potentially imprinted placental genes, many showing preferentially paternal expression. Within a core set of 15 genes with verified imprinting patterns, two-thirds of genes had paternal expression, according to tests on samples from the horse-donkey hybrids and comparisons with expression profiles in each parent species.

Nevertheless, the team noted that paternally expressed and maternally silent genes from placenta tissue did not necessarily have parent-of-origin expression biases in the hybrid offspring themselves. Moreover, some of the apparently imprinted genes showed distinct imprinting profile from one individual to the next, even within the same species.

That variability, said the study's authors, "results in a unique epigenetic signature for each placenta that contributes to variation in the intra-uterine environment and thus presents the opportunity for natural selection to operate on parent-of-origin differential regulation."

An international team led by investigators in Germany, Switzerland, and the UK has found evidence suggesting that the genetic diversity present within the leprosy-causing bacterial species Mycobacterium leprae has remained relatively stable over the past 1,000 years or more.

As they explained in Science, the researchers relied on a bead capture method to screen for M. leprae genetic material in 22 medieval skeletons found in the UK, Sweden, and Denmark. They subsequently focused on bone and teeth samples from five of the skeletons, using array capture to nab stretches of the M. leprae genome for sequencing.

The team then put the whole or partial genome sequences obtained from those ancient isolates up against sequences from 11 modern-day M. leprae strains collected around the world, and a side-by-side comparison revealed unexpected conservation within the pathogen's genome.

That apparent constancy belies the marked decline in leprosy cases around the world since the late Middle Ages, authors of the study noted, hinting that human adaptations may have bolstered our defenses against the long-feared pathogen.

"If the explanation of the drop in leprosy cases isn't in the pathogen, then it must be in the host, that is, in us; so that's where we need to look," co-senior author Stewart Cole, a researcher with Ecole Polytechnique Fédérale de Lausanne's Global Health Institute, said in a statement.

"In certain conditions, victims could simply be pressured not to procreate," he noted. "In addition, other studies have identified genetic causes that made most Europeans more resistant than the rest of the world population, which also lends credence to this hypothesis."