The Continuing Evolution of the Xenopus Genome

• Published in: Xenopus pp. 155 - 171
• Main Authors: Kondo, Mariko, Taira, Masanori
• Format: Book Chapter
• Language: English
• Published: CRC Press 2022
• Edition: 1
• Subjects: Xenopus; DNA Transposon; homeolog; Genus Xenopus; rDNA Cluster; Ivory Coast; allotetraploid; Comprehensive Gene Expression Analyses; Genome Duplication; Pg DNA; Molecular Biological Approaches; Xenopus borealis; Homeologous Chromosomes; whole genome sequence; heterosis; African Clawed Frog Xenopus Laevis; nucleolar dominance; Xenopus tropicalis; Gene Clusters; High Nucleotide Identities; asymmetric evolution; Xenopus laevis; subgenome; whole genome duplication; Hox Genes; hybrid; Hox Clusters; African Clawed Frog; Xenopus Species; subgenome dominance; rDNA Gene Cluster; Fosmid Clones; Fish Analysis
• ISBN: 9780367505271; 0367505274; 0367505347; 9780367505349
• DOI: 10.1201/9781003050230-12

The African clawed frog, Xenopus laevis, has been used as a model animal since the 1930s to study various subjects by biochemical and molecular biological approaches. X. laevis has advantages as a model animal, some of which may be owing to X. laevis being allotetraploid. However, gene redundancy due to allotetraploidy was recognized as a disadvantage since the late 1990s, when developmental genetics dominated the field of developmental biology. The size and complexity of this genome were also disadvantages for whole genome analysis. In 2016, thanks to improved technologies and reduction of costs for sequencing and to the inbred strain J, the entire genome structure as well as subgenomes, called L and S, of X. laevis were revealed. Detailed analyses of gene organization in the subgenomes, such as retention rates of homeolog pairs and paralogous gene expansions, including the rDNA cluster, demonstrated asymmetric evolution of subgenomes, in which L is more conserved than the S genome. Since then, allotetraploid genome analyses have opened a new research field in animals by shedding light on subgenome evolution after allopolyploidization, which may also provide insights into what happened in the two rounds of whole genome duplication (WGD) during vertebrate evolution, as well as in the third round of WGD in the common ancestor of teleosts. We will discuss the historical background of genome studies of Xenopus laevis, its contributions to science, and future directions. The African clawed frog, Xenopus laevis, has been used as a model animal since the 1930s to study various subjects by biochemical and molecular biological approaches. X. laevis has advantages as a model animal, some of which may be owing to X. laevis being allotetraploid. The evolutionary history of Xenopus frogs leading to the current phylogenetic relationships consist of bifurcating speciation and allopolyploidization by interspecies hybridization followed by polyploidization. Heterosis, or hybrid vigor, is observed in hybrids that have superior phenotypes such as more vigorous growth or higher progeny yields compared to their parents. Whole genome sequencing is a powerful tool for analyzing the evolution of the genome. It can also reveal the full genetic make-up of an organism, allowing for comprehensive analysis of the relationships among many genes and their regulatory sequences. The hox genes and the Hox clusters are often identified and characterized for genome analysis or evolutionary studies.