Regular readers might remember the weird case of Oxytricha, a ciliate that eliminates 95% of the DNA in its genome after sexual reproduction using transposases. The latest PNAS contains a report by Smith et al. of a similar genomic reorganization in the sea lamprey (Petromyzon marinus). In the lamprey, 20% of its genome, or about 500 million nucleotides, are removed from the somatic cells. The full genome is retained in the germ line (the cells that eventually become sperm and ova). To put that in perspective, the entire rice genome is smaller than the amount of DNA removed from the lamprey's somatic cells. It's about 100 times bigger than the genome of E. coli K12. That's a lot of DNA.
Smith et al. tracked the occurrence of specific sequences eliminated from the somatic cells. One such sequence, Germ1 is suddenly eliminated at gastrulation. Another sequence (a SPOPL homologue) is gradually lost during the entire course of development. There's probably more than one mechanism removing this DNA, which is even more mind-boggling.
I'm yet again amazed at how little we understand how genomes work and do what they do. In our naive Mendelian way, we like to think of genomes as neat collections of genes, each of which codes for a trait. As an organism goes through development, genes are switched on and off at the appropriate time to make the adult critter. Lampreys wonderfully defy that simplicity, and who knows what else we might find. Perhaps there are other organized genomic reorganizations that can occur that we have yet to discover.
Smith et al. 2009. Programmed loss of millions of base pairs from a vertebrate genome. PNAS 106:11212-11217.