Comparative transcriptome analysis identified important genes and regulatory pathways for flower color variation in Paphiopedilum hirsutissimum

Abstract

Background Paphiopedilum hirsutissimum is a member of Orchidaceae family that is famous for its ornamental value around the globe, it is vulnerable due to over-exploitation and was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents its trade across borders. Variation in flower color that gives rise to different flower patterns is a major trait contributing to its high ornamental value. However, the molecular mechanism underlying color formation in P. hirsutissimum still remains unexplored. In the present study, we exploited natural variation in petal and labellum color of Paphiopedilum plants and used comparative transcriptome analysis as well as pigment measurements to explore the important genes, metabolites and regulatory pathways linked to flower color variation in P. hirsutissimum. Result We observed that reduced anthocyanin and flavonoid contents along with slightly higher carotenoids are responsible for albino flower phenotype. Comparative transcriptome analysis identified 3287 differentially expressed genes (DEGs) among normal and albino labellum, and 3634 DEGs between normal and albino petals. Two genes encoding for flavanone 3-hydroxylase (F3H) and one gene encoding for chalcone synthase (CHS) were strongly downregulated in albino labellum and petals compared to normal flowers. As both F3H and CHS catalyze essentially important steps in anthocyanin biosynthesis pathway, downregulation of these genes is probably leading to albino flower phenotype via down-accumulation of anthocyanins. However, we observed the downregulation of major carotenoid biosynthesis genes including VDE, NCED and ABA2 which was inconsistent with the increased carotenoid accumulation in albino flowers, suggesting that carotenoid accumulation was probably controlled at post-transcriptional or translational level. In addition, we identified several key transcription factors (MYB73, MYB61, bHLH14, bHLH106, MADS-SOC1, AP2/ERF1, ERF26 and ERF87) that may regulate structural genes involved in flower color formation in P. hirsutissimum. Importantly, over-expression of some of these candidate TFs increased anthocyanin accumulation in tobacco leaves which provided important evidence for the role of these TFs in flower color formation probably via regulating key structural genes of the anthocyanin pathway. Conclusion The genes identified here could be potential targets for breeding P. hirsutissimum with different flower color patterns by manipulating the anthocyanin and carotenoid biosynthesis pathways.

Abiotic factors and endophytes co-regulate flavone and terpenoid glycoside metabolism in Glycyrrhiza uralensis

“…7 , several genes involved in the flavonoid backbone production, such as Glyur001446s00035041 encoding cinnamate 4-hydroxylase (C4H) and Glyur000681s00027307 encoding 4-coumarate-CoA ligase (4CL), were up-regulated in both 21H-CK and 21H-GUH21. The up-regulation of these enzymatic DEGs was probably due to the enhanced expression of two TFs, including bHLH14 ( Glyur000099s00014930 ) and MYB39-like ( Glyur000423s00024443 ), which were transcriptional activators of flavonoid biosynthetic genes, such as C4H and CHS (Zhang et al 2015 ; Li et al 2021 ). Meanwhile, ERF2 ( Glyur000067s00006346 ), a potential transcription activator of ROS scavenging genes (Yang et al 2021 ), was significantly up-regulated in both 21H-CK and 21H-GUH21, suggesting that the high watering amount had the function to regulate the redox balance in G. uralensis roots.…”

Comprehensive identification and analysis of circRNAs during hickory (Carya cathayensis Sarg.) flower bud differentiation

“…We performed GO enrichment analysis for the host genes of DE circRNAs to better understand how circRNA may be involved in flower development. GOseq (version 2.12) was used to annotate the function of the parent genes of the differentially expressed circRNAs’ host genes ( Young et al., 2010 ) using the Wallenius non-central hyper-geometric distribution method ( Kang and Liu, 2015 ; Bedre et al., 2019 ; Lipka et al., 2019 ; Li et al., 2021 ). The Benjamini Hochberg method was used to correct the p-value, with a smaller value being more significant.…”

Phenotypic and transcriptome profiling of spikes reveals the regulation of light regimens on spike growth and fertile floret number in wheat

“…Meanwhile, 102 functional DEGs, including numerous MYB transcription factors, were predicted to interact directly with CO-like. These functional DEGs were mainly involved in jasmonic acid, salicylic acid and auxin responses (e.g., Zm38, MYB1, MYB61, MYB308, Zm1, MYB4 and MYB16; Li et al, 2021;Zhou et al, 2022) and anther wall tapetum development (e.g., MYB80 and MYB35; Phan et al, 2011;Zhu et al, 2008) (Figure 6d,e). In addition, other genes, such as CRYD, mitochondrial (Castrillo et al, 2013), and SWEET2B, a member of the bidirectional SWEET sugar transporter family (Ji et al, 2022), also cooperated with CO-like genes to accelerate flower development under LW treatment (Figure 6d).…”