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.

AUXIN/INDOLE ACETIC ACIDs (Aux/IAAs), an early auxin-responsive gene family, is important for plant growth and development. To fully comprehend the character of Aux/IAA genes in woody plants, we identified 19 PmIAA genes in Prunus mume and dissected their protein domains, phylogenetic relationship, gene structure, promoter, and expression patterns during floral bud flushing, auxin response, and abiotic stress response. The study showed that PmIAA proteins shared conserved Aux/IAA domain, but differed in protein motif composition. 19 PmIAA genes were divided into six groups (Groups Ⅰ to Ⅵ) based on phylogenetic analysis. The gene duplication analysis showed that segmental and dispersed duplication greatly influenced the expansion of PmIAA genes. Moreover, we identified and classified the cis-elements of PmIAA gene promoters and detected elements that are related to phytohormone responses and abiotic stress responses. With expression pattern analysis, we observed the auxin-responsive expression of PmIAA5, PmIAA17, and PmIAA18 in flower bud, stem, and leaf tissues. PmIAA5, PmIAA13, PmIAA14, and PmIAA18 were possibly involved in abiotic stress responses in P. mume. In general, these results laid the theoretical foundation for elaborating the functions of Aux/IAA genes in perennial woody plant development.

The Gibberellic Acid Stimulated Arabidopsis/Gibberellin Stimulated Transcript (GASA/GAST) gene family is a group of plant-specific genes encoding cysteine-rich peptides essential to plant growth, development, and stress responses. Although GASA family genes have been identified in various plant species, their functional roles in Prunus mume are still unknown. In this study, a total of 16 PmGASA genes were identified via a genome-wide scan in Prunus mume and were grouped into three major gene clades based on the phylogenetic tree. All PmGASA proteins possessed the conserved GASA domain, consisting of 12-cysteine residues, but varied slightly in protein physiochemical properties and motif composition. With evolutionary analysis, we observed that duplications and purifying selection are major forces driving PmGASA family gene evolution. By analyzing PmGASA promoters, we detected a number of hormonal-response related cis-elements and constructed a putative transcriptional regulatory network for PmGASAs. To further understand the functional role of PmGASA genes, we analyzed the expression patterns of PmGASAs across different organs and during various biological processes. The expression analysis revealed the functional implication of PmGASA gene members in gibberellic acid-, abscisic acid-, and auxin-signaling, and during the progression of floral bud break in P. mume. To summarize, these findings provide a comprehensive understanding of GASA family genes in P. mume and offer a theoretical basis for future research on the functional characterization of GASA genes in other woody perennials.

‘Diacylglycerol acyltransferase (DGAT)’ acts as a key rate-limiting enzyme that catalyzes the final step of the de novo biosynthesis of triacylglycerol (TAG). The study was to characterize the function of the DGAT3 gene in Paeonia rockii, which is known for its accumulation of high levels of unsaturated fatty acids (UFAs). We identified a DGAT3 gene which encodes a soluble protein that is located within the chloroplasts of P. rockii. Functional complementarity experiments in yeast demonstrated that PrDGAT3 restored TAG synthesis. Linoleic acid (LA, C18:2) and α-linolenic acid (ALA, C18:3) are essential unsaturated fatty acids that cannot be synthesized by the human body. Through the yeast lipotoxicity test, we found that the yeast cell density was largely increased by adding exogenous LA and, especially, ALA to the yeast medium. Further ectopic transient overexpression in Nicotiana benthamiana leaf tissue and stable overexpression in Arabidopsis thaliana indicated that PrDGAT3 significantly enhanced the accumulation of the TAG and UFAs. In contrast, we observed a significant decrease in the total fatty acid content and in several major fatty acids in PrDGAT3-silenced tree peony leaves. Overall, PrDGAT3 is important in catalyzing TAG synthesis, with a substrate preference for UFAs, especially LA and ALA. These results suggest that PrDGAT3 may have practical applications in improving plant lipid nutrition and increasing oil production in plants.

Callose is an important polysaccharide composed of beta-1,3-glucans and is widely implicated in plant development and defense responses. Callose synthesis is mainly catalyzed by a family of callose synthases, also known as glucan synthase-like (GSL) enzymes. Despite the fact that GSL family genes were studied in a few plant species, their functional roles have not been fully understood in woody perennials. In this study, we identified total of 84 GSL genes in seven plant species and classified them into six phylogenetic clades. An evolutionary analysis revealed different modes of duplication driving the expansion of GSL family genes in monocot and dicot species, with strong purifying selection constraining the protein evolution. We further examined the gene structure, protein sequences, and physiochemical properties of 11 GSL enzymes in Prunus mume and observed strong sequence conservation within the functional domain of PmGSL proteins. However, the exon–intron distribution and protein motif composition are less conservative among PmGSL genes. With a promoter analysis, we detected abundant hormonal responsive cis-acting elements and we inferred the putative transcription factors regulating PmGSLs. To further understand the function of GSL family genes, we analyzed their expression patterns across different tissues, and during the process of floral bud development, pathogen infection, and hormonal responses in Prunus species and identified multiple GSL gene members possibly implicated in the callose deposition associated with bud dormancy cycling, pathogen infection, and hormone signaling. In summary, our study provides a comprehensive understanding of GSL family genes in Prunus species and has laid the foundation for future functional research of callose synthase genes in perennial trees.

Corrigendum: Genome-wide identification of Aux/IAA gene family and their expression analysis in Prunus mume