Chromosome‐scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata

Abstract

Summary Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high‐quality chromosome‐scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein‐coding genes. Second, our metabolome analyses uncovered pelargonidin‐3‐O‐glucoside, cyanidin‐3‐O‐arabinoside, and cyanidin‐3‐O‐glucoside as the main pigments involved in leaf color transition. Third, gene co‐expression further identified the MYB‐bHLH‐WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co‐expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high‐quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

Integrated transcriptomics and metabolomics analyses provide insights into anthocyanin biosynthesis for leaf colour formation in Quercus mongolica

“…Anthocyanin biosynthesis is a branch of the avonoid synthesis pathway starting from phenylalanine, and involving a variety of enzymes encoded by early biosynthesis genes (PAL, 4CL, C4H, CHS, CHI, F3H, F3'H, and F3'5'H) and anthocyanin biosynthesis genes (DFR, ANS, and UFGT) [39]. Previous studies have shown that several key genes and enzymes are required for anthocyanin accumulation and leaf colour formation in many ornamental plants, such as Quercus dentata [40] and cassava (Manihot esculenta) [41].…”

A haplotype-resolved reference genome ofQuercus albasheds light on the evolutionary history of oaks

“…The first published oak genome was that of Quercus robur (Plomion et al ., 2016a), the pedunculate oak, which is common throughout western Eurasia. To date, there have been at least nine Quercus species with published chromosome-scale genomes, including four annotated genomes from the white oak clade (Plomion et al ., 2016a; Han et al ., 2022; Liu et al ., 2022; Sork et al ., 2022; Zhou et al ., 2022; Ai et al ., 2022; Kapoor et al ., 2023; Wang et al ., 2023). This growing number of annotated genomes allows for comparative analyses of gene content and inferences of genome evolution across the oak phylogeny.…”

Karyotype and LTR-RTs analysis provide insights into oak genomic evolution

“…As an important ecological and economic tree in East Asia, oaks are famous for their environmental adaptability, resistance to biotic and abiotic stresses, and providing many biological materials [ 35 , 36 ]. Currently, eight chromosome-level oak genomes have been sequenced and annotated, including Q. acutissima [ 37 ], Q. dentata [ 38 ], Q. gilva [ 39 ], Q. glauca [ 40 ], Q. lobata [ 41 ], Q. mongolica [ 42 ], Q. robur [ 11 ], and Q. variabilis [ 43 ]. These provide a comprehensive database for analysing the genomic and chromosomal evolution of the genus.…”