A book draft before printing often carries extra pages: marginal notes, repetitions, crossed-out paragraphs. The print shop doesn't include them, but the author keeps them in case of revisions. The genome of the nematode Auanema rhodense works in much the same way: its germ cells hold the complete draft at 180.9 megabases, while the body cells retain only 60 megabases of clean text. That's a threefold difference, and it doesn't arise by chance but according to a strict plan.
When the embryo reaches the 12-cell stage, DNA begins to be cut in four of the eight blastomeres. Giant blocks of tandem repeats drop out of the chromosomes: identical stretches sitting one after another, like pages with a repeated line. The breaks occur at 28 sites, and each one carries a palindromic motif 29 nucleotides long. This motif is almost identical to the one found in the related species Oscheius tipulae, but the scale differs: in O. tipulae only 0.6% of the genome is discarded, while in A. rhodense it is 61%.
By the 30-cell stage, almost all nuclei have already lost the repeats, and only two nuclei keep them: these are the future germ cells. The discarded DNA consists almost entirely of tandem repeats with a unit length ranging from 167 to 504 nucleotides. There are few protein-coding genes in it: only 360 out of 11,943, and most of them resemble the remnants of mobile elements. Only ten of the discarded genes are actively expressed, and nearly all of them have working copies in the somatic part of the genome.
It used to be thought that programmed DNA elimination was an exotic feature of parasitic ascarids, where the breaks are imprecise and lack motifs. Now it's clear that the mechanism arose in the common ancestor of the rhabditids and then diverged: in some species it is barely noticeable, while in others, as in A. rhodense, it turns the body genome into a heavily trimmed copy. The precision of motif recognition is preserved, while the amount of discarded DNA varies.
A draft from which the rough pages are torn out before printing: that's one way to describe this process. In the germ cells, the draft is kept whole, so that all variants can be passed on to descendants. In the body cells, only what is needed for life here and now remains. And although no applications for this knowledge are in sight yet, a precise map of the elimination sites could become the basis for synthetic systems of controlled DNA removal in biotechnology.
Auanema rhodense has three sexes: males, females and hermaphrodites. What is more, males pass on only the X chromosome to their offspring, while hermaphrodites produce only sperm carrying two X chromosomes, whereas their eggs contain no X at all.
The idea of cells deliberately throwing away part of their genetic material echoes the motif of forbidden knowledge in science fiction: in Greg Bear's novel Blood Music, for instance, cells rearrange their DNA and acquire a will of their own. Here, though, everything is under the control of evolution rather than rebellion.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.