A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa

Abstract

Chaenomeles speciosa (2 n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.

Acknowledgements

This work was supported by the Key Industries Innovation Chain Major Project, Hubei Province (2021ACA004 and 2022 AC003-01- 003).

Author contributions

X.Y., X.W., and S.S. conceived the project. S.H., D.W., Y.Z., Q.K., K.W., N.J., F.L., Y.G., H.X., L.W., S.F., and Z.M. participated in the data analysis. S.H., Y.Z., Q.K., D.X., and S.S. wrote the manuscript. All authors have read and approved the final version of the paper.

Data availability

The whole genome sequence data reported in this paper have been deposited in the NCBI BioProject under accession number PRJNA890604 and NCBI BioSample under accession number SAMN31283309. The genome data referred in this article: Rosa chinensis (NCBI: GCF_002994745.2), Prunus armeniaca (NCBI: GCA_020424065.1), Prunus persica (NCBI: GCA_000346465.2), Pyrus communis BartlettDHv2.0 (PyrusCommunis_BartlettDHv2.0, http://peargenome.njau.edu.cn/), Malus domestica (NCBI: GCA_004115385.1), Prunus yedoensis (NCBI: GCA_002966975.2), Carica papaya (NCBI:GCF_000150535.2), Vitis vinifera (NCBI: GCA_000003745.2), Pyrus betulifolia (NGDC:GWHAAYT00000000), Arabidopsis thaliana (NCBI: GCF_000001735.4).

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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