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Genomics in the Journals Oct 9, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, Spanish researchers reported on the recombination events contributing to Legionella pneumophila outbreaks in Spain over more than a decade.

The team did SOLiD 5500XL whole-genome sequencing on 69 L. pneumophila clinical or environmental isolates collected during more than a dozen outbreaks in the Spanish city of Alcoy between 1999 and 2010.

Patterns in these genomes pointed to at least 16 recombination events in the L. pneumophila collection, consistent with five different branch-off points in the bug's short-term evolution. That recombination appears to have introduced more than 2,000 SNPs into the core genome of the L. pneumophila sequence type ST578, the researchers explained, apparently fueling L. pneumophila's variability in the region.

"In the case of L. pneumophila, we have shown that accelerated evolution in the environment is linked to recombination events," they wrote. "If the relative contribution of recombination in the generation of genetic variation in a population demonstrated in these analyses is confirmed for other bacterial populations and species, we must conclude that the adaptive and evolutionary relevance of recombination for bacteria is even greater than previously appreciated."


For another Nature Genetics study, an international team led by researchers at the University of Montreal described mutations in the chromosome cohesion-related gene SGOL1 that can cause a newly described heart and gut condition dubbed "chronic atrial and intestinal dysrhythmia," or CAID, which they diagnosed in 16 French Canadians and a single individual from Sweden.

The team did whole-exome sequencing on three individuals with CAID, a condition characterized by a combination of symptoms related to altered pacemaker activity in the heart and gut. In the heart, this leads to symptoms resembling those found in a heart condition called sick sinus syndrome (SSS), while the gut effects resemble a rare intestinal malady known as chronic intestinal pseudo-obstruction (CIPO).

An analysis of protein-coding sequences from the three affected individuals led to a homozygous SGOL1 mutation found in all three of them. The researchers subsequently saw the same genetic glitch in the remaining 14 CAID patients through targeted gene sequencing experiments, and used zebrafish model experiments to link lower-than-usual levels of the SGOL1 gene to symptoms resembling those found in the patients.

On the other hand, the mutation turned up with a minor allele frequency south of 1 percent in public sequence databases and was not detected in exome sequences from 360 unaffected French Canadian controls. Nor was it present in dozens of pediatric patients suffering from either SSS or CIPO alone.

With the help of genealogical data, the team found clues that the CAID cases considered for the study can be traced back to a founder couple in France in the early 1600s, who themselves inherited the mutation separately as the result of Viking migrations centuries earlier between Scandinavia and what is now Normandy, France.


A study in the American Journal of Human Genetics considered the extent to which alterations converging on shared molecular pathways could manifest themselves in different neurodevelopmental disorders.

A McGill University-led team did RNA sequencing, reduced representation bisulfite sequencing, chromatin immunoprecipitation sequencing, and genome-wide microRNA assays on human neural progenitor cells designed to model two neurodevelopmental conditions: 9q34 deletion syndrome and 18q21 deletion syndrome.

From these experiments, the researchers concluded that there is at least some molecular overlap between 9q34 deletion syndrome — which arises due to haploinsufficiency of the methyltransferase enzyme-coding gene EHMT1 — and 18q21 deletion syndrome, a condition known as Pitt-Hopkins syndrome that's caused by haploinsufficiency of the transcription factor coding gene TCF4.

For instance, they noted that EHMT1 and TCF4 share a significant proportion of their respective gene targets, despite the gene expression and methylation differences detected for the two neurodevelopmental conditions.

Based on their findings, the study's authors argued that "[c]ommon intersection points might highlight the most salient features of disease and provide avenues for similar treatments for [neurodevelopmental disorders] caused by different genetic mutations."


Southern California freeways and other forms of human development are contributing to a dip in genetic diversity amongst mountain lions (also called pumas or cougars) in that area, according to a PLOS One study by researchers based at the University of California at Davis and the Nature Conservancy.

When they looked at the big cats' genetic patterns by region using information at dozens of microsatellite loci for 354 mountain lions from sites spanning California, the investigators saw especially low genetic diversity amongst the 97 mountain lions living in the Santa Ana Mountains south of Los Angeles compared with mountain lions sampled at other sites in the state.

Given the timing of the apparent genetic bottleneck in that population, the team argued that human developments over the past 80 years or so — including the introduction of an interstate that separates Santa Ana mountain lions from cats in the neighboring range — have impacted the animals' genetic diversity.

Moreover, co-author Winston Vickers, a veterinarian at the UC Davis Wildlife Health Center, argued that such unanticipated wildlife impacts "can happen anywhere."

"If we keep building without attention to these issues, we're going to keep creating more pockets of isolation where animals can no longer connect with each other," he said in a statement.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.