Abstract
Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.
Highlights
Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates
We sequenced the tetraploid genomes of three distinct C. carpio strains, namely, Hebao red carp (HB) and Yellow River carp (YR) from China, which belong to the subspecies C. carpio haematopterus, and German mirror carp (GM) from Europe, which belongs to the subspecies C. carpio carpio, by whole-genome shotgun methods (Supplementary Fig. 1, Supplementary Table 1)
Three chromosome-level reference genomes of C. carpio were created with high connectivity, representing 1.24 Gb (82%) of HB, 1.26 Gb (89%) of YR and 1.3 Gb (92%) of GM assemblies, respectively (Supplementary Table 4)
Summary
Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. To assess the selective pressure of two subgenomes, we calculated both the nonsynonymous substitution rate (Ka) and Ks values based on homoeologous gene pairs (Supplementary Data 5).
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