Dynamic transcriptome and network-based analysis of yellow leaf mutant Ginkgo biloba

Abstract

Background Golden leaf in autumn is a prominent feature of deciduous tree species like Ginkgo biloba L., a landscape tree widely cultivated worldwide. However, little was known about the molecular mechanisms of leaf yellowing, especially its dynamic regulatory network. Here, we performed a suite of comparative physiological and dynamic transcriptional analyses on the golden-leaf cultivar and the wild type (WT) ginkgo to investigate the underlying mechanisms of leaf yellowing across different seasons. Results In the present study, we used the natural bud mutant cultivar with yellow leaves “Wannianjin” (YL) as materials. Physiological analysis revealed that higher ratios of chlorophyll a to chlorophyll b and carotenoid to chlorophyll b caused the leaf yellowing of YL. On the other hand, dynamic transcriptome analyses showed that genes related to chlorophyll metabolism played key a role in leaf coloration. Genes encoding non-yellow coloring 1 (NYC1), NYC1-like (NOL), and chlorophyllase (CLH) involved in the degradation of chlorophyll were up-regulated in spring. At the summer stage, down-regulated HEMA encoding glutamyl-tRNA reductase functioned in chlorophyll biosynthesis, while CLH involved in chlorophyll degradation was up-regulated, causing a lower chlorophyll accumulation. In carotenoid metabolism, genes encoding zeaxanthin epoxidase (ZEP) and 9-cis-epoxy carotenoid dioxygenase (NCED) showed significantly different expression levels in the WT and YL. Moreover, the weighted gene co-expression network analysis (WGCNA) suggested that the most associated transcriptional factor, which belongs to the AP2/ERF-ERF family, was engaged in regulating pigment metabolism. Furthermore, quantitative experiments validated the above results. Conclusions By comparing the golden-leaf cultivar and the wide type of ginkgo across three seasons, this study not only confirm the vital role of chlorophyll in leaf coloration of YL but also provided new insights into the seasonal transcriptome landscape and co-expression network. Our novel results pinpoint candidate genes for further wet-bench experiments in tree species.

Molecular Mechanisms of Chlorophyll Deficiency in Ilex × attenuata ‘Sunny Foster’ Mutant

“…The differentially expressed TFs identified in our study belonged to gene families such as bHLHs, NACs, MYB-related, ERFs, B3s, C2H2s, GRASs, LBDs, MYBs, WRKYs, and GLKs. Similar findings were reported in a yellow-leaf mutant of G. biloba [28]. The suppression of bHLH71-like in pepper plants led to elevated levels of zeaxanthin and antheraxanthin, implying a role for bHLH71-like as a promoter of Car biosynthesis in the yl1 yellow pepper mutant [90].…”

“…× 'Whoa Nellie' unveiled alterations in chloroplast ultrastructure and reduced gene expression linked to Chl biosynthesis and photosynthesis, leading to Chl deficiency in the mutant leaves [24]. Similarly, transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) profiling in Ginkgo biloba identified differentially expressed genes (DEGs) involved in pigment metabolism and putative transcription factors (TFs) associated with its leaf coloration [28]. Through an integrated transcriptomic and metabolomic investigation in Cucumis melo, enzyme genes and metabolites predominantly associated with central carbon metabolism, photosynthesis, flavonoid metabolism, and energy metabolism were identified [29].…”

Transcriptome and Biochemical Analyses of a Chlorophyll-Deficient Bud Mutant of Tea Plant (Camellia sinensis)

“…A similar increased expression of CLH2 was also found to be related to the reduced chlorophyll contents in a leaf-color mutant of Cymbidium sinense [24]. In the yellow-leaf bud mutant cultivar 'Wannianjin' of Ginkgo biloba, dynamic transcriptome analyses suggested that both the decreased expression of the biosynthesis gene, i.e., HEMA, and the increased expression of the degradation gene (CLH) caused a low chlorophylls accumulation [25]. Meanwhile, a previous study indicated that the upregulated expression of the CLH and NYC1 genes in the yellow-green leaf WY16-13 of wucai (Brassica campestris) germplasm might have accelerated the degradation of the chlorophylls, resulting in the yellowing of the plant's leaves [26].…”

Effects of different light intensity on leaf color changes in a Chinese cabbage yellow cotyledon mutant

“…In the downstream process of carotenoid metabolism, a list of enzymes can cleave carotenoid to produce phytohormone abscisic acid (ABA) and strigolactones, and the downregulated expression of these downstream genes had been extensively demonstrated to be involved in the catabolism of carotenoid ( Nisar et al., 2015 ; Yuan et al., 2015 ). The expression of NCED gene in ginkgo was increased in yellow leaves in autumn, while decreased in green leaves in summer ( Sun et al., 2022 ). Previous studies in zucchini reported that NCED and CCD genes were downregulated in yellow and orange peels, which was agreement with the accumulation of yellow lutein ( Obrero et al., 2013 ; Niu et al., 2023 ).…”