Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

Abstract

Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. We constructed a high-density genetic linkage map with an average map distance of 0.33 cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains CDL15, CRG98, and GID1b1 associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L. indica, with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.

Acknowledgements

This work was supported by National Key R&D Program of China (2019YFD1001004, 2019YFD1000402), the program for Science and Technology of Beijing (Z181100002418006) and the Special Fund for Beijing Common Construction Project.

Author contributions

Q.X.Z., H.T.P., and T.R.C. conceived and designed experiments. Y.Z., T.C.Z., M.C., L.F., X.W., C.Q.Y., M.Z., Y.H., and J.W. collected all materials and phenotypic data. Y.Z., T.C.Z., and M.C. contributed to genome sequencing and assembly. Y.Z., T.C.Z., X.F.C., P.S., and Z.T.W. contributed to SNP calling, population analysis, genetic map construction, transcriptome sequencing, and BSA analysis. Y.Z., T.C.Z., and H.T.P. wrote the manuscript. Q.X.Z. and T.R.C. revised and finalized the manuscript. All authors approved the manuscript before submission.

Data availability

The final assembly and annotation of the L. indica genome, the whole-genome sequences, raw resequencing data of populations, and raw transcriptome RNA-seq data are available at the National Genomics Data Centre (NGDC) under BioProject ID PRJCA013427.

Conflict of interest

The authors declare that they have no conflict of interest.

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