To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ‘fossil’ transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17–18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

Mechanics of follicle patterning in skin: Studies of skin organogenesis have presupposed that a periodic molecular prepattern is responsible for the initiation of a periodic pattern of hair or feathers. To date, however, these initiating molecules have remained elusive. Using chicken skin as a model system, Shyer et al. found that the periodic spacing of feathers is triggered by mechanical rather than molecular events (see the Perspective by Grill). Furthermore, these mechanical events shape both the structure of prefeathers and their molecular identity. Science , this issue p. 811 ; see also p. 750

The frog Xenopus , an important research organism in cell and developmental biology, currently lacks tools for targeted mutagenesis. Here, we address this problem by genome editing with zinc-finger nucleases (ZFNs). ZFNs directed against an eGFP transgene in Xenopus tropicalis induced mutations consistent with nonhomologous end joining at the target site, resulting in mosaic loss of the fluorescence phenotype at high frequencies. ZFNs directed against the noggin gene produced tadpoles and adult animals carrying up to 47% disrupted alleles, and founder animals yielded progeny carrying insertions and deletions in the noggin gene with no indication of off-target effects. Furthermore, functional tests demonstrated an allelic series of activity between three germ-line mutant alleles. Because ZFNs can be designed against any locus, our data provide a generally applicable protocol for gene disruption in Xenopus .

Programmed cell death is important for the proper development of the retina, and microRNAs (miRNAs) may be critical for its regulation. Here, we report that miR-24a is expressed in the neural retina and is required for correct eye morphogenesis in Xenopus. Inhibition of miR-24a during development causes a reduction in eye size due to a significant increase in apoptosis in the retina, whereas overexpression of miR-24a is sufficient to prevent apoptosis. We show that miR-24a negatively regulates the proapoptotic factors caspase9 and apaf1, demonstrating a role for miRNAs in the regulation of apoptosis during normal development.