A telomere-to-telomere gap-free reference genome of Chionanthus retusus provides insights into the molecular mechanism underlying petal shape changes

Abstract

Chionanthus retusus, an arbor tree of the Oleaceae family, is an ecologically and economically valuable ornamental plant for its remarkable adaptability in landscaping. During C. retusus breeding, we observed diverse floral shapes; however, no available genome for C. retusus has hindered the widespread identification of genes related to flower morphology. Thus, a de novo telomere-to-telomere (T2T) gap-free genome was generated. The assembly, incorporating high-coverage and long-read sequencing data, successfully yielded two complete haplotypes (687 and 683 Mb). The genome encompasses 42 864 predicted protein-coding genes, with all 46 telomeres and 23 centromeres in one haplotype. Whole-genome duplication analysis revealed that C. retusus underwent one fewer event of whole-genome duplication after differentiation compared to other species in the Oleaceae family. Furthermore, flower vein diversity was the main reason for the differences in floral shapes. Auxin-related genes were responsible for petal shape formation on genome-based transcriptome analysis. Specifically, the removal and retention of the first intron in CrAUX/IAA20 resulted in the production of two transcripts, and the differences in the expression levels of CrAUX/IAA20 resulted in the variations of flower veins. Compared to transcripts lacking the first intron, transcripts with intron retention caused more severe decreases in the number and length of flower veins in transgenic Arabidopsis thaliana. Our findings will deepen our understanding of flower morphology development and provide important theoretical support for the cultivation of Oleaceae.

Acknowledgements

This work was supported by the Subject of Key R & D Plan of Shandong Province (Major Scientific and Technological Innovation Project) Mining, Accurate Identification of Forest Tree Germplasm Resources (No. 2021LZGC023) and Agricultural science and Technology Fund Project of Shandong province (No. 2019LY001-4).

Author contributions

X.H. and J.L. conceived and supervised the study. D.X. performed genome assembly and annotation. C.L. and J.W. performed phenotypic analysis of C. retusus petals. M.S., Y.L., and J.W. performed experiments for functional validation of CrAUX/IAA20. Y.S. and J.W. performed transcriptome analyses. M.N. performed gene phenotype correlation analysis. M.S., Y.L., L.L., and J.W. prepared the plant tissue for sequencing. J.W., D.X., X.H., and J.L. wrote the manuscript.

Data availability

The Hi-C and ONT data, as well was the assemblies have been deposited to National Genomics Data Center with Bioproject ID of CRA011999. The RNA-seq data have been deposited to China National GeneBank DataBase with Bioprojrct ID of CNP0005081.

Conflict of interest statement

The authors declare that they have no competing interests.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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