Integrative Metabolomic and Transcriptomic Analyses Reveal the Mechanism of Petal Blotch Formation in Rosa persica.

Petal blotch is a specific flower color pattern commonly found in angiosperm families. In particular, Rosa persica is characterized by dark red blotches at the base of yellow petals. Modern rose cultivars with blotches inherited the blotch trait from R. persica. Therefore, understanding the mechanism for blotch formation is crucial for breeding rose cultivars with various color patterns. In this study, the metabolites and genes responsible for the blotch formation in R. persica were identified for the first time through metabolomic and transcriptomic analyses using LC-MS/MS and RNA-seq. A total of 157 flavonoids were identified, with 7 anthocyanins as the major flavonoids, namely, cyanidin 3-O-(6″-O-malonyl) glucoside 5-O-glucoside, cyanidin-3-O-glucoside, cyanidin 3-O-galactoside, cyanidin O-rutinoside-O-malonylglucoside, pelargonidin 3-O-glucoside, pelargonidin 3,5-O-diglucoside, and peonidin O-rutinoside-O-malonylglucoside, contributing to pigmentation and color darkening in the blotch parts of R. persica, whereas carotenoids predominantly influenced the color formation of non-blotch parts. Zeaxanthin and antheraxanthin mainly contributed to the yellow color formation of petals at the semi-open and full bloom stages. The expression levels of two 4-coumarate: CoA ligase genes (Rbe014123 and Rbe028518), the dihydroflavonol 4-reductase gene (Rbe013916), the anthocyanidin synthase gene (Rbe016466), and UDP-flavonoid glucosyltransferase gene (Rbe026328) indicated that they might be the key structural genes affecting the formation and color of petal blotch. Correlation analysis combined with weighted gene co-expression network analysis (WGCNA) further characterized 10 transcription factors (TFs). These TFs might participate in the regulation of anthocyanin accumulation in the blotch parts of petals by modulating one or more structural genes. Our results elucidate the compounds and molecular mechanisms underlying petal blotch formation in R. persica and provide valuable candidate genes for the future genetic improvement of rose cultivars with novel flower color patterns.

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

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.

Transcriptome profiling to identify tepal cell enlargement and pigmentation genes and the function of LtEXLB1 in Lilium tsingtauense.

To understand the molecular mechanism underlying tepal development and pigmentation in Lilium tsingtauense Gilg, we performed whole-transcriptome profiles from closed buds at the greenish tepal stage (CBS), the full-bloom with un-horizontal tepal stage (UFS), and the completely opened bud with reflected tepal stage (RFS) of L. tsingtauense. More than 95699 transcripts were generated using a de novo assembly approach. Gene ontology and pathway analysis of the assembled transcripts revealed carbon metabolism is involved in tepal development and pigmentation. In total, 8171 differentially expression genes (DEGs) in three tepal stages were identified. Among these DEGs, ~994 genes putatively encoded transcription factors (TFs), whereas 693 putatively encoded protein kinases. Regarding hormone pathways, 51 DEGs involved in auxin biosynthesis and signalling and 10 DEGs involved in ethylene biosynthesis and signalling. We also isolated seven LtEXPANSINs, including four EXPAs, one EXPB, one EXLA and one EXLB. LtEXLB1 (GenBank: MN856627) was expressed at higher levels in UFS and RFS, compared with CBS. Silencing LtEXLB1 in leaf discs and tepals by virus-induced gene silencing significantly decreased cell expansion under rehydration conditions. Further analysis revealed that more cell numbers were existed in the abaxial and adaxial subepidermis in the silenced LtEXLB1 samples. As the first transcriptome of L. tsingtauense, the unigenes are a valuable resource for future studies on tepal development, and LtEXLB1 functions in cell expansion.