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

Crape myrtle (Lagerstroemia indica), a widely cherished ornamental plant, boasts a rich history, originating in Southeast Asia to Oceania and flourishing in cultivation centers like China for over 1600 years. Renowned for its unique blooming during the summer peak, it has evolved through extensive hybridization, and now includes more than 200 species. Current research has made strides in understanding the determinants of plant architecture, flower, leaf color, and dwarfism traits through transcriptomics and QTL mapping. However, the absence of a reference genome for L. indica severely limits comprehensive genomic studies. This gap hinders the exploration of molecular mechanisms underlying key traits and impedes advancements in plant evolution, domestication, and genomic breeding.

In July 2023, Horticulture Research published a research article entitled by “Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle ”.  

In this study,  the first high-quality genome assembly of Lagerstroemia indica (L. indica) was performed utilizing PacBio sequencing and Hi-C scaffolding. The genome annotation identified 33,608 genes and around 42.19% of the genome as repetitive elements. Comparative genomic analysis with 17 species mapped gene families, uncovering 3,572 genes unique to L. indica. Evolutionary analysis revealed a recent whole-genome triplication in L. indica, and a phylogenetic tree positioned L. indica with L. speciosa and P. granatum in Myrtales. Population structure analysis of 73 accessions using SNPs revealed the evolutionary history and breeding of modern crape myrtle cultivars. Principal component analysis and pairwise sequential Markovian coalescent showed rich polymorphism among species, with distinct fluctuations in population size. The study of linkage disequilibrium and Tajima's D values highlighted the increased genetic diversity in cultivar accessions. A high-density genetic linkage map for L. indica was created using an F1 population of L. fauriei and L. indica ‘Pocomoke’. This map contained 5,660 SNP markers divided into 24 linkage groups. QTL analysis of plant architecture traits identified 33 intervals affecting phenotypic variation, with a major-effect interval on LG1 significantly influencing internode length. For flower color, transcriptome sequencing of flowers of different colors identified a large number of DEGs involved in flavonoid pathways essential for petal color determination. Additionally, bulk segregant analysis mapped leaf color loci to chr12 and chr17, and identified five candidate genes, including homologs to MYB35, NCED, and KAS1, related to pigmentation.

In conclusion, this study not only elucidates L. indica's genome and evolutionary history but also provides insights into the genetic basis of its ornamental traits, offering a foundation for future research and molecular breeding in Myrtaceae.

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References

Authors

Yang Zhou^†, Tangchun Zheng^†, Ming Cai^†, Lu Feng, Xiufeng Chi, Ping Shen, Xin Wang, Zhiting Wan, Cunquan Yuan, Man Zhang, Yu Han, Jia Wang, Huitang Pan^*, Tangren Cheng^*, and Qixiang Zhang^*

†These authors contributed equally to this work.

Affiliations

Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing

About Qixiang Zhang

He is currently the vice president of Beijing Forestry University University, and has long been engaged in teaching and research work on flowers, and carried out sustained and systematic research in the excavation of plum blossoms, chrysanthemums, and other important flower germplasm, cultivation of varieties, and industrialization technology.