The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Xu, P.; Xu, J.; Liu, G.; Chen, L.; Zhou, Z.; Peng, W.; Jiang, Y.; Zhao, Z.; Jia, Z.; Sun, Y.; Wu, Y.; Chen, B.; Pu, F.; Feng, J.; Luo, J.; Zhang, H.; Wang, H.; Dong, C.; Jiang, W.; Sun, X.

doi:10.1101/498774

bioRxiv · 10.1101/498774

The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio

Xu, P.·Xu, J.·Liu, G.·Chen, L.·Zhou, Z.·Peng, W.·Jiang, Y.·Zhao, Z.·Jia, Z.·Sun, Y.·Wu, Y.·Chen, B.·Pu, F.·Feng, J.·Luo, J.·Zhang, H.·Wang, H.·Dong, C.·Jiang, W.·Sun, X.

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Abstract

Common carp (Cyprinus carpio) is an allotetraploid Cyprinid species derived from recent whole genome duplication and provides an excellent model system for studying polyploid genome evolution in vertebrates. To explore the origins and consequences of tetraploidy in C. carpio, we generated three chromosome-level new reference genomes of C. carpio and compared them to the related diploid Cyprinid genome sequences. We identified a progenitor-like diploid Barbinae lineage by analysing the phylogenetic relationship of the homoeologous genes of C. carpio and their orthologues in closely related diploid Cyprinids. We then characterized the allotetraploid origin of C. carpio and divided its genome into two homoeologous subgenomes that are marked by a distinct genome similarity to their diploid progenitor. On the basis of the divergence rates of homoeologous genes and transposable elements in two subgenomes, we estimated that the two diploid progenitor species diverged approximately 23 million years ago (Mya) and merged to form the allotetraploid C. carpio approximately 12.4 Mya, which likely correlated with environmental upheavals caused by the extensive uplift of the Qinghai-Tibetan Plateau. No large-scale gene losses or rediploidization were observed in the two subgenomes. Instead, we found extensive homoeologous gene expression bias across twelve surveyed tissues, which indicates that subgenome B is dominant in homoeologous expression. DNA methylation analysis suggested that CG methylation in promoter regions plays an important role in altering the expression of these homoeologous genes in allotetraploid C. carpio. This study provides an essential genome resource and insights for extending further investigation on the evolutionary consequences of vertebrate polyploidy.

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Xu, P., Xu, J., Liu, G., Chen, L., Zhou, Z., Peng, W., Jiang, Y., Zhao, Z., Jia, Z., Sun, Y., Wu, Y., Chen, B., Pu, F., Feng, J., Luo, J., Zhang, H., Wang, H., Dong, C., Jiang, W., Sun, X.. 2018-12-29. The allotetraploid origin and asymmetrical genome evolution of common carp Cyprinus carpio. https://doi.org/10.1101/498774

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