Genome evolution in the allotetraploid frog Xenopus laevis

Abstract

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 demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved 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.

Filaggrin has evolved from an “S100 fused‐type protein” (SFTP) gene present in a common ancestor of amphibians and mammals

“…We screened newly available genome sequence assemblies of the African clawed frog, Xenopus laevis, [18,19] and other amphibians for SFTP genes (see Supplementary Information). The expression of genes in tissues of X. laevis was determined by RT-PCR.…”

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

“…Species of the African Clawed frog Xenopus provide an ideal system to study hybridization and genome evolution. Xenopus laevis is an allotetraploid with 36 chromosomes that arose through interspecific hybridization of diploid progenitors, whereas Xenopus tropicalis is a diploid with 20 chromosomes that diverged from a common ancestor ~48 million years ago 3 . Differences in genome size between the two species are accompanied by organism size differences, and size scaling of the egg and subcellular structures such as nuclei and spindles formed in egg extracts 4 .…”

Genomic innovation for crop improvement

“…Proximity ligation is a method that physically links segments of DNA that are in close proximity in chromatin by chemical cross-linking in vivo, which is followed by ligation of the adjacent DNA sequences and sequencing of the ligated regions. The proximity-based ligation of nuclear-chromatin preparations generates contact probability maps that link DNA sequence reads across Mb scales while identifying various chromosomal compartments and interactions 36,37 . The HaploSeq method used proximity ligation coupled to low-coverage (17×) Illumina sequencing to generate extended haplotypes of the human genome 38 .…”