![]() ![]() We annotated 45,099 protein-coding genes and 342 microRNAs using RNA sequencing (RNA-seq) from 14 developmental stages (including the oocyte stage) and 14 adult tissues and organs ( Supplementary Note 4), analysis of histone marks associated with transcription, and homology with X. laevis genes and assigns >91% of the assembled sequence (and 90% of the predicted protein-coding genes) to a chromosomal location. These complementary methods produced a high-quality chromosome-scale draft that includes all previously known X. laevis inbred ‘J’ strain by whole-genome shotgun methods in combination with long-insert clone-based end sequencing, ( Supplementary Note 2) and organized the assembled sequences into chromosomes using fluorescence in situ hybridization (FISH) of 798 bacterial artificial chromosome clones (BACs) and in vivo and in vitro chromatin conformation capture analysis ( Supplementary Note 3 and Methods). Superimposed on these global trends are local gene family expansions and the alteration of gene expression patterns. ![]() Despite sharing the same nucleus, we find that the subgenomes have evolved asymmetrically: one of the two subgenomes has experienced more intrachromosomal rearrangement, gene loss by deletion and pseudogenization, and changes in levels of gene expression and in histone and DNA methylation. The two subgenomes are distinct and maintain separate recombinational identities. laevis genome from its extinct progenitor diploids. Here we provide evidence for the allotetraploid hypothesis by tracing the origins of the X. 1 for discussion of the Xenopus allotetraploidy hypothesis). laevis has a chromosome number (2 n = 36) nearly double that of the Western clawed frog Xenopus (formerly Silurana) tropicalis (2 n = 20) and most other diploid frogs 12, and is proposed to be an allotetraploid that arose via the interspecific hybridization of diploid progenitors with 2 n = 18, followed by subsequent genome doubling to restore meiotic pairing and disomic inheritance 10, 13 (see Supplementary Note 1 and Extended Data Fig. laevis is one of a polyploid series that ranges from diploid to dodecaploid, and is therefore ideal for studying the impact of genome duplication 10, especially given its status as a model for cell and developmental biology 11. However, the component subgenomes of a polyploid must cooperate to mediate potential incompatibilities of dosage, regulatory controls, protein–protein interactions and transposable element activity. Polyploidy provides raw material for evolutionary diversification because gene duplicates can support new functions and networks 9. While polyploidy is rare in amniotes, presumably owing to constraints on sex chromosome dosage 3, 4, it is common in fish 5, amphibians 6, 7, and plants 8. Nature volume 538, pages 336–343 ( 2016) Cite this articleĪncient polyploidization events have shaped diverse eukaryotic genomes 1, including two rounds of whole-genome duplication at the base of the vertebrate radiation 2. Genome evolution in the allotetraploid frog Xenopus laevis ![]()
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