Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression

Abstract

Cassava is a crucial crop that makes a significant contribution to ensuring human food security. However, high-quality telomere-to-telomere cassava genomes have not been available up to now, which has restricted the progress of haploid molecular breeding for cassava. In this study, we constructed two nearly complete haploid resolved genomes and an integrated, telomere-to-telomere gap-free reference genome of an excellent cassava variety, ‘Xinxuan 048’, thereby providing a new high-quality genomic resource. Furthermore, the evolutionary history of several species within the Euphorbiaceae family was revealed. Through comparative analysis of haploid genomes, it was found that two haploid genomes had extensive differences in linear structure, transcriptome features, and epigenetic characteristics. Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway. The high heterozygosity of cassava ‘Xinxuan 048’ leads to rapid trait segregation in the first selfed generation. This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.

Acknowledgements

This work was supported by the National Natural Science Foundation of China (32100526, 32270712), the Guangxi Natural Science Foundation (AD23026047), the Young Elite Scientists Sponsorship Program by CAST (2022QNRC001), the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (SKLCUSA-a202205, SKLCUSA-a03), Ba-Gui Scholar Program of Guangxi (To Z.G. H), the Project of Bama County for Talents in Science and Technology (20220008), Chief Expert of Tuberous Crops Innovation Team in Guangxi Province (nycytxgxcxtd-2023-11-01) and the starting research grant for High-level Talents and Innovation and development multiplication plan from Guangxi University (2022BZRC015).

Author contributions

J.M.S., L.L.C., and H.B.Y. conceived and designed the study. L.L., X.H.S., P.S., W.Z., S.C., and Z.D.W. contributed to sample preparation. X.D.X., R.P.Z., L.X., M.G., Y.H.L., Z.W.Z., S.Y.Y., Y.Q.Q., and B.L.F. participated in data analysis and substantively revised the manuscript. All authors read and approved the final manuscript.

Data availability

The original sequencing and assembly of the cassava variety XX048 genome is available from the National Genomics Data Center [77] under project number PRJCA016162.

Conflict of interest

The authors declare that they have no conflict of interest.

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