The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes

Abstract

Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.

Acknowledgments

We thank André Marques (Max Planck Institute for Plant Breeding Research) for his valuable comments on ChIP-seq analysis. We thank Jianming Zeng (University of Macau), and all the members of his bioinformatics team, biotrainee, for generously sharing their experience and codes. We thank Yangqin Xie for his suggestions. We thank Tian Li for helping to deposit the data. We also thank all members of our group.

This project was supported by the National Natural Science Foundation of China (32101544), and the Chongqing Research Pro-gram of Basic Research and Frontier Technology (cstc2021yszx-jcyj0004).

Author contributions

Conceptualization, B.M. and N.H.; funding and resources, B.M., N.H; data production, formal analyses, investigation, and visualization, B.M.; experimentation, H.W., J.L., L.C., X.X.; sample preparation, B.M., H.W., J.L., X.X., W.W., Z.Y., J.Y., Y.L; writing, B.M.; review and editing: N.H. All authors read and approved the final manuscript.

Data availability

All the raw sequencing data and genome assembly generated for this project are deposited at Nation Genomics Data Center under BioProject no. PRJCA015883, and the genome assembly and annotations are also deposited at MorusDB (https://morus.swu.edu.cn). All the materials in this study are available upon request.

Conflict of interest statement

No conflicts of interest declared.

Supplementary data

Supplementary data is available at, Horticulture Research online.

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