Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color

Abstract

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

Acknowledgements

This work was supported by grants from the Strategic Priority Research Program, Chinese Academy of Sciences (Grant No. XDA23080000) and Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502).

Author contributions

F.-S.Y and J.-F.M planned and designed the research. S.N., S.-W.Z, T.-L.S., W.Z., R.-G.Z., X.-C.T., J.-F.G., X.-M.Y., Y.-T.B., Z.-C.L, L.K., H.-Y.M., Z.-Y.C., and H.L. performed experiments, conducted fieldwork, analysed data etc. J.-F.M., F.-S.Y. and S.N. wrote the manuscript; I.P. and Y.A.E.-K. were involved in finalizing the manuscript draft.

Data availability

The genome assembly, annotation, and raw sequence data have been deposited in NCBI (https://www.ncbi.nlm.nih.gov/) with the accession number JAKSEO000000000 (BioProject: PRJNA804375). The whole genome assembly, gene and repeat element annotations have been deposited in the Genome Warehouse in the National Genomics Data Center (https://ngdc.cncb.ac.cn/gwh/) under BioProject number PRJCA012078.

Conflict of interests

The authors declare no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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