The crop genomes cometh

There has been a sudden rash (well two!) of published whole crop genomes this week, the fruit of the improvements in sequencing efficiency brought to us by the '2nd gen.' sequencing technologies.

The wheat genome will prove very interesting, as it's the first huge multi-ploid crop genome to be sequenced. Wheat is thought to be a hexaploid, evolved from a hybrid of three different ancestral cereal genomes. Assembly of the small fragments of a genome like this is a bioinformatician's nightmare. First, such a huge genome contains enormous numbers of repeat regions due to proliferation of 'selfish' DNA transposable elements. In addition, the genome contains several copies of most of the genes, originating from the three ancestral genomes, and figuring out which is which is rather tricky. How did the group who have published manage to do it? Well I'm not sure they actually did. It seems that what has been published is a set of unassembled 454 short reads providing 5-fold coverage of the genome as a whole. Millions upon millions of short fragments. Very useful information, but not quite a whole genome. We will see what we can make of that.

It was also announced that the Golden Delicious apple genome has been sequenced. Apples are evolutionarily very interesting, as they are very highly heterozygous - rampant outcrossers - which is why they never come true from seed. All the real Golden Delish out there are clones of a single genome that grew up in America, possibly from a seedling spread in waste from cider presses. But that's another story for another time.