Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution

Abstract

The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars ‘Veitchii’ and ‘Endless Summer’ [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F₁ hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.

Acknowledgments

The research presented in this article was supported in part by funds from the Floral and Nursery Research Initiative adminis-tered through the United States Department of Agriculture, Agri-cultural Research Service (USDA-ARS). The work was supported by USDA-ARS CRIS project numbers 6066-21310-005-00D and 8020-21000-072-000-D. The authors would like to thank Carrie Witcher for assistance with pollen collection and microscopy and Dr Jerry Jenkins from the HudsonAlpha Institute for Biotechnology for his technical advice on scaffolding. Benjamin Moore and Joseph Davis maintained the plants used in this experiment. This research used resources provided by the SCINet project of the USDA Agricultural Research Service, ARS project numbers 0500-00093-001-00-D and 5030-21000-069-00D. The mention of trade names of commercial products in the publication is solely for the purpose of provid-ing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.

Author Contributions

X.W., L.W.A., and A.M.H.-K. developed the project. X.W. and A.M.H-K. performed all analyses. S.A.S., R.C.Y., X. F.L, and B.E.S. per-formed the sequencing. L.W.A. and T.A.R. generated plant popula-tions and provided support. X.W., L.W.A., and A.M.H.-K. wrote the manuscript. All authors read and approved the final manuscript.

Data Availability

All data supporting the findings in this study are available within this article and its additional files. The reference genome raw sequencing data, whole-genome sequencing data, RNA-seq data, and genome assembly data have been deposited at the NCBI Sequence Read Archive under BioProject number PRJNA675507 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA675507). Addi-tional details can be found at https://github.com/USDA-ARS-GBRU/Hydrangea_Genomes.

Conflict of Interests

The authors declare that they have no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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