Mac’s highlights from NSA
The 104th meeting of the National Shellfisheries Association was held last week in the always lovely Seattle, WA. I think I have about a million pages of notes and highlights, but I will try to be concise here and just mention a few things that I found particularly interesting.
1) The impending Crassostrea gigas genome. In Tuesday morning’s plenary, Dennis Hedgecock (USC) presented a summary of the assembled C. gigas genome (manuscript is currently in review). A few stats: The C. gigas genome has more that 28,000 genes; ~35% of the genome is comprised of repetative elements; the genome contains lots of transposable elements - and they’re active; relative to humans, C. gigas has an abundance of genes involved in transcription and translation.
2) Genomics on a budget. For those poor folks who are still working with non-models, Eli Meyer (OSU) presented cost-effective approaches for transcriptome and genotype analysis using high-throughput sequencing. He discussed the 3’ tag-based RNA-Seq approach used in Meyers et al 2011 and also an updated RAD procedure. The new “2b-RAD” utilizes Type IIb restriction enzymes to generate small fragments of exactly the same length. He noted that representation could be reduced even further by an additional tagging step that would mark 1/16th of the library for sequencing.
3) Oyster epigenetics. Guillaume Riviere presented data from his lab examining the role of DNA methylation during larval development in C.gigas. They were able to show that total DNA methylation varied at different larval stages and that expression of certain DNA methyltransferases and methyl-binding domain proteins were stage-specific. Using an interesting combination of MeDIP and qPCR they found an inverse relationship between DNA methylation and expression level of Hox genes in oyster larvae. After the talks we had some great discussions about the challenges and directions of epigenetics research in shellfish. Pretty exciting stuff.