Uncommon Ground ably unpacks Nature paper on grapevine genome.
DNA barcoding takes off
DNA barcoding is based on a gamble (or maybe a shrewd guess), and perhaps a smidgin of circular thinking: that there is a chunk of genome short enough to sequence quickly and cheaply, and which shows just enough variability for the entire sequence to be the same for all members of a species, but different for different species. Well, the gamble seems to have paid off. A suitable bit of a gene has duly been identified for both animals and plants, data are being ammassed, and there’s talk of a portable gadget being available in a few years which will read off the relevant sequence from a bit of leaf or skin or something and compare it with a database to give you the species name right there in the field.
More “contaminated” bison
The ancestors of the bison, or buffaloes, of Catalina Island off the California coast arrived as movie extras in 1924. Scientists have always thought they were more likely to be pure-bred than many of the other buffalo that roam North America, because they’ve effectively been in isolation. Turns out it ain’t so. Nearly half the animals shipped off the island have maternal cow genes. Scientists believe the cross breeding probably occurred before the buffalo were shipped to Catalina — and nothing since 1924 has selected against it.
P.S. As the commenter to our original piece pointed out, nobody seems to have looked for bison genes in cattle. Why not?
Colony collapse disorder culprit?
The mysterious ailment afflicting bee hives may be caused by a virus, Israeli acute paralysis virus of bees, IAPV ((This is bound to be all over the media, and I’m stuck in an airport without good access, but after our semi-exhaustive coverage of the great bee shortage it wouldn’t do to ignore the news completely.)). That’s the conclusion of a report just published online in Science Express ((D.L. Cox-Foster et al. (2007) A metagenomic survey of microbes in honey bee colony collapse disorder doi:10.1126/science.1146498))
In some respects the technique was dead simple. The researchers took samples from hives that had CCD, hives that didn’t have CCD, and royal jelly. They bulked up all the DNA in the samples and threw it into a very fast sequencer to decode all of it. Computer programs then assembled the various bits and pieces and compared them to all known genes. And the result? Evidence of a whole bunch of bacteria, fungi, animals and viruses, almost all of them equally present in CCD and non-CCD colonies. But one virus — Israeli acute paralysis virus — was found in almost all the CCD samples and only one non-CCD sample.
IAPV is related to Kashmir bee virus and was first described in Israel in 2004. The first recent reports of CCD date to 2004. Of course there are many other factors at work too, including the influence of pesticides and the presence of Varroa mites and the chemicals used to control them, to say nothing of possible changes in climate. As the researchers cautiously note:
We have not proven a causal relationship between any infectious agent and CCD; nonetheless, the prevalence of IAPV sequences in CCD operations, as well as the temporal and geographic overlap of CCD and importation of IAPV-infected bees, indicate that IAPV is a significant marker for CCD.
That’ll do for now. And there’s no mention of mobile phones.
Wheat disease genes
Fusarium graminearum is the fungus that causes Fusarium head blight, a serious disease of wheat and barley. FHB infects the flowers and makes itself at home in the seed, which ends up shrunken and white and loaded with toxins that can have a harmful effect on people and animals that eat the grain. A study just published in Science decoded the DNA sequence of the fungus and sheds some light on its virulence and variability ((The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization. Science: 317:1400 – 1402 DOI: 10.1126/science.1143708)).
The sequence of one strain is interesting enough, but the surprises emerged when the researchers, led by Corby Kistler at the University of Minnesota, compared two different strains. There were more than 10,000 differences between the two sequences. Those differences, however, were not spread evenly along the DNA; more than half of the differences were concentrated in just one eighth of the sequence.
So some regions of the genome are much less stable than others. And what genes are in those regions? Mostly ones concerned with infection and virulence, among them the genes for compounds that dissolve the host cell walls and others that digest host molecules so that the fungus can make use of them.
Just why the variability in Fusarium graminearum is concentrated in some areas of the DNA is not yet clear. These areas seem to be hotspots for recombination, which shuffles the DNA during sexual reproduction and so promotes diversity, but this particular fungus doesn’t go in for sexual reproduction all that often. A mystery, then, but one that may still yield new approaches to breeding resistant wheat and barley and perhaps to new kinds of treatment.
You may remember that a joint team of Israeli and US researchers recently reported that a wild relative of wheat, Sharon Goatgrass (Aegilops sharonensis), is loaded with resistance genes that protect it against seven of the most important fungal diseases of wheat. Alas, none of the samples tested was resistant to Fusarium head blight. How about some other wild relative species, though? We shall see.