Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Abstract

Background: Akebia trifoliata (Thunb.) Koid may have applications as a new source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

Comparative Transcriptome and Proteome Analysis Provides New Insights Into the Mechanism of Protein Synthesis in Kenaf (Hibiscus cannabinus L.) Leaves

“…The data presented here are sufficient and accurate and will provide useful guidance tools for the study of protein synthesis in kenaf leaves and other mallow plants. In addition, there were a lot of “predicted,” “putative,” or “uncharacterized” transcripts and proteins in the annotation results, suggesting that the nature of the analysis was restricted because of the lack of detailed genomic information ( Niu et al, 2020 ). As a result, the functions of these unknown or unidentified genes and proteins in the protein synthesis of kenaf leaves should be explored in further researches.…”

The Akebia Genus as a Novel Forest Crop: A Review of Its Genetic Resources, Nutritional Components, Biosynthesis, and Biological Studies

“…Recent studies have focused on fruit cracking and flesh softening, which are consequential of multiple cellular processes. Microscopic results suggest that the structure and texture of the cell wall changed significantly during the initial cracking stage, such as thinner and looser cell walls, fewer cell layers, and increased space between cells in the pericarp (Niu et al, 2020;Jiang et al, 2022). Although significant changes in physiology and biochemistry have been observed during fruit cracking in A. trifoliata, such as the depolymerization of covalently bound pectin and cellulose, disordered ROS (reactive oxygen species) homeostasis, decrease in minerals (K and Ca), degradation of starch, and water movement, these changes may be regulated by phytohormones through increased indole-3acetic acid (IAA), salicylic acid, and jasmonic acid levels, as well as decreased cytokinin content (Jiang et al, 2022).…”

“…The molecular foundation for unsaturated fatty acid biosynthesis was also revealed by the transcriptome and metabolic profiles. The FA and TAG biosynthetic pathways were reconstructed, and the expression pattern of key genes during the development of seeds was uncovered, such as acetyl-CoA carboxylase (ACCase), fattyacid synthase (FAS), three acyl-ACP thioesterases (FATA/B), and three long-chain acyl-CoA synthetases (LACS), which play an essential role in fatty-acid biosynthesis, chain termination, Niu et al (2020Niu et al ( , 2021.…”