Third generation technologies are making more genomes feasible
April 28 2017
Two plant genomes showed up this week in Nature publications - lettuce and barley. This late in the genome game, it takes some extra pizzazz to get a genome in Nature… so why two plants? Because they are examples of what third generation technologies can do!
Lettuce - Near Chromosome Scale Assembly via Hi-C
Dovetail is in the news again, this time in helping UC Davis and BGI researchers assemble the 2.7Gb lettuce genome, following up on the success of the goat and mosquito genomes at similar chromosome level resolution. However, this is still a big deal in plants, which have larger genomes, less strong relationships between physical and genetic distance, and high repeat content. These genomes have been intractible for a very long time. The HiC/cHiCago maps provide large scale scaffolds at low resolution to assist in mapping short, higher accuracy/resolution reads - thus overcoming issues of repeats (which tend to be shorter than map length, but longer than short reads). Combining mapping technologies with reads has been a popular way of dealing with this issue - with clear success.
Barley - Near Chromosome Scale via Kitchen Sink
Some plants aren't just plagued by large genomes with high repeat content, they have additional issues that limit the accessibility of the genome. Barley is plagued by a very specific issue - limited recombination in large tracks of the genome. These large chunks limit the resolution of a genetic map in providing spacial context for genes, and additionally limit the ability to use the genetic map to help scaffold sequences. However, using chromosome flow sorting, the chromosomes were isolated, then sequenced - effectively breaking up the large genome into small sections (see MutChromSeq paper). The resulting assembly represents ~95% of the 4.79Gb genome using BioNano Irys, Dovetail Hi-C, BACs sequenced in 454 and Illumina short reads, and a genetic map assisted by MutChromSeq leveraged from the large amount of population sequencing in barley.
For more on how Third Generation Sequencing has impacted plant genomics, see this paper!