<b>Genome Evolution and Subgenome Partitioning in Cypriniformes</b>
<p dir="ltr">While all vertebrates have experienced two rounds of WGD (1R and 2R), ray-finned fishes have undergone an additional one known as the teleost-specific genome duplication (TSGD or 3R). Certain lineages within ray-finned fish, such as those in the orders Cypriniformes and...
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2025
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| Summary: | <p dir="ltr">While all vertebrates have experienced two rounds of WGD (1R and 2R), ray-finned fishes have undergone an additional one known as the teleost-specific genome duplication (TSGD or 3R). Certain lineages within ray-finned fish, such as those in the orders Cypriniformes and Salmoniformes, have undergone further rounds of WGDs, contributing to evolutionary diversification. The evolutionary mechanisms and consequences of WGD in Cypriniformes have been extensively studied, particularly in fishes like the common carp and goldfish, with a focus on subgenome splitting, asymmetry, and functional divergence. However, other polyploid species within Cypriniformes remain relatively underexplored, limiting our understanding of the broader evolutionary impacts of WGD across this order. Here, we present newly assembled chromosome-level genomes for two loach species—<i>Sinibotia superciliaris</i> (Golden Chinese Loach) and <i>Parabotia fasciatus</i> (Yichang Sand Loach)—and integrate them into a comparative genomic analysis of 20 other species within the Cypriniformes. This study aims to resolve phylogenetic relationships and examine subgenome partitioning, providing critical insights into the origins and evolutionary mechanisms of polyploid formation. We reveal that polyploid species within the Cypriniformes, including loaches and carps, do not share a monophyletic origin and diverged across multiple evolutionary timelines. Our new approach to subgenome partitioning (M3) introduces a new method for subgenome division. Additionally, we investigate genome size reduction and its association with positively selected genes in a clade consisting of two subgenomes from Golden Chinese Loach and wide-bodied sand loach (<i>Sinibotia reevesae</i>). In conclusion, this study provides new insights into subgenome evolution in Cypriniformes species, highlighting the complex dynamics of polyploidy.</p> |
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