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Genomics in the Journals: Jul 18, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, an international team led by investigators at the University of Zurich reported on findings from a genome sequencing study of a fungal pathogen called wheat powdery mildew, or Blumeria graminis forma specialis tritici.

The researchers started by generating a draft genome sequence for the fungus using BAC contigs, Roche 454 sequencing, and genomic DNA from a B. graminis f.sp. tritici isolate called 96224. Within the resulting reference sequence, which spanned some 82 million bases or so of the organism's 180 million base genome, they tracked down 6,540 predicted protein-coding genes and a slew of transposable element sequences.

By resequencing three more wheat powdering mildew strains from Switzerland, England, and Israel and comparing them to the new reference sequence, meanwhile, the group was able to assess genetic diversity in the fungus. It also got clues to the pathogen's evolutionary past — both before and after the availability of domesticated wheat as a host plant.

Findings from the latter analysis hint that present-day wheat powdering mildew genomes are a mash-up of ancient haplogroups kicking around before wheat was domesticated some 10,000 years ago. "We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a diverse haplotype pool that provided great genetic potential for pathogen variation," said the study's authors.

Mutations in an enzyme-coding gene called DSTYK can lead to a type of congenital abnormality characterized by kidney or urinary tract malformations, according to a study in the New England Journal of Medicine.

A Columbia University-led team identified an alteration in the dual serine/threonine and tyrosine protein kinase gene through linkage analysis on individuals from a multi-generational Sardinian family with a form of the condition inherited in an autosomal dominant manner. The researchers also performed whole-exome sequencing on two of the seven affected family members.

The search led to a heterozygous mutation in DSTYK that turned up in all of the affected family members. The genetic glitch did was not detected in unaffected individuals from the family or in unrelated individuals from the Sardinian or European populations.

The researchers also unearthed alterations in DSTYK in seven of the 311 unrelated individuals with congenital kidney or urinary tract malformation conditions that they tested by targeted sequencing, suggesting mutations in the gene account for at least a subset of such cases.

"These findings indicate that DSTYK mutations account for 2.2 percent of urinary tract defects in humans, which is very significant as a single-gene cause of this disease," Columbia's Simone Sanna-Cherchi, first author on the study, said in a statement.

A research duo from Vanderbilt University garnered evidence that suggests constituents of gut microbial communities can influence speciation in their host organism — an apparent example of so-called hologenomic adaptation that the pair presented in the early, online edition of Science.

By focusing on three jewel wasp species from the genus Nasonia, the team determined that microbiome composition differs in the guts of non-viable offspring produced via crosses between different Nasonia species.

In particular, the investigators' hybrid crossing, genotyping, and other experiments indicated that wasps from N. vitripennis species tend to show high rates of hybrid lethality when crossed with either N. giraulti or N. longicornis — two species from which N. vitripennis diverged around a million years ago. In contrast, the two more closely related species produced viable hybrid offspring in most instances.

But survival of offspring from jewel wasp hybrid crosses seemed to rely on more than just the genetics of the host species themselves, the team noted. Hybrid offspring that survived typically had gut microbiomes resembling those in parental species, while those that perished showed distinct shifts in gut microbial community composition. In addition, survival improved dramatically for the offspring of germ-free N. vitripennis wasps crossed with wasps from the N. giraulti or N. longicornis species.

"The expectation in the field was that the origin of species is principally driven by genetic changes in the nucleus," senior author Seth Bordenstein, a biology, pathology, microbiology, and immunology researcher at Vanderbilt, said in a statement. "Our study demonstrates that both the nuclear genome and the microbiome must be considered in a unified framework of speciation."

In another Science study, researchers from France and Sweden described massive viruses from a genus that they call Pandoravirus, which appear to be only distantly related to other very large viruses found in the past.

The two Pandoraviruses characterized for the study — one collected at the bottom of an Australian freshwater pond and another from a sediment sample taken off Chile's central coast — had genomes containing between 1.9 million bases and more than 2.5 million bases.

The new viruses, dubbed Pandoravirus dulcis and Pandoravirus salinus appear to be parasites of the single-celled Acanthamoeba. Nevertheless, the researchers' morphological assessments and genome sequencing studies of P. salinus and P. dulcis suggested that the Pandoraviruses share fairly scant similarities to other hefty viruses that infect the amoeba.

"This work is a reminder that our census of the microbial diversity is far from comprehensive," the study's authors wrote, "and that some important clues about the fundamental nature of the relationship between the viral and the cellular world might still lie within unexplored environments."