Transcriptomic and metabolomic analyses of non-structural carbohydrates in red maple leaves

Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Mechanism of Red Maple (Acer rubrum L.) Leaf Coloring

This study employed a combination of ultraviolet spectrophotometry, LC-ESI-MS/MS system, and RNA-sequencing technology; the extracts and isolation of total RNA from the red and yellow leaf strains of red maple (Acer rubrum L.) at different developmental stages were subjected to an intercomparison of the dynamic content of chlorophyll and total anthocyanin, flavonoid metabolite fingerprinting, and gene expression. The metabonomic results indicated that one hundred and ninety-two flavonoids were identified, which could be classified into eight categories in the red maple leaves. Among them, 39% and 19% were flavones and flavonols, respectively. The metabolomic analysis identified 23, 32, 24, 24, 38, and 41 DAMs in the AR1018r vs. AR1031r comparison, the AR1018r vs. AR1119r comparison, the AR1031r vs. AR1119r comparison, the AR1018y vs. AR1031y comparison, the AR1018y vs. AR1119y comparison, and the AR1031y vs. AR1119y comparison, respectively. In total, 6003 and 8888 DEGs were identified in AR1018r vs. AR1031r comparison and in the AR1018y vs. AR1031y comparison, respectively. The GO and KEGG analyses showed that the DEGs were mainly involved in plant hormone signal transduction, flavonoid biosynthesis, and other metabolite metabolic processes. The comprehensive analysis revealed that caffeoyl-CoA 3-O-methyltransferase (Cluster-28704.45358 and Cluster-28704.50421) was up-regulated in the red strain but down-regulated in the yellow strain, while Peonidin 3-O-glucoside chloride and Pelargonidin 3-O-beta-D-glucoside were up-regulated in both the red and yellow strains. By successfully integrating the analyses on the behavior of pigment accumulation, dynamics of flavonoids, and differentially expressed genes with omics tools, the regulation mechanisms underlying leaf coloring in red maple at the transcriptomic and metabolomic levels were demonstrated, and the results provide valuable information for further research on gene function in red maple.

The chromosome-scale genome provides insights into pigmentation in Acer rubrum

Acer rubrum L. is one of the most prevalent ornamental species of the genus Acer, due to its straight and tall stems and beautiful leaf colors. For this study, the Oxford Nanopore platform and Hi-C technology were employed to obtain a chromosome-scale genome for A. rubrum. The genome size of A. rubrum was 1.69 Gb with an N50 of 549.44 Kb, and a total of 39 pseudochromosomes were generated with a 99.61% genome. The A. rubrum genome was predicted to have 64644 genes, of which 97.34% were functionally annotated. Genome annotation identified 67.14% as the transposable element (TE) repeat sequence, with long terminal repeats (LTR) being the richest (55.68%). Genome evolution analysis indicated that A. rubrum diverged from A. yangbiense ∼6.34 million years ago. We identified 13 genes related to pigment synthesis in A. rubrum leaves, where the expressions of four ArF3'H genes were consistent with the synthesis of cyanidin (a key pigment) in red leaves. Correlation analysis verified that the pigmentation of A. rubrum leaves was under the coordinated regulation of non-structural carbohydrates and hormones. The genomic sequence of A. rubrum will facilitate genomic breeding research for this species, while providing the valuable utilization of Aceraceae resources.