- Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. - Analysis of the TF – DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. - Further analysis of the DEG – SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Full list of author information is available at the end of the article. - heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. - Albino mutations are common in the plant kingdom. - In albino leaf tissue of Hydrangea macrophylla, com- bined metabolome and transcriptome analyses revealed the changed genes and metabolites were significantly enriched in the chlorophyll synthesis pathway and TCA cycle in response to albinism [2]. - In Arabidopsis thali- ana albino mutants, the altered genes and metabolites after plant albinism were mainly involved in the TCA cycle and the oxidative pentose phosphate pathway in response to albinism [3]. - heterophyllus albino mutants [8, 9]. - Therefore, the integration of metabolomics and transcriptomics can provide a system-wide understanding of the transcriptomic and metabolic changes in A. - Analysis of transcriptome data. - The FLNC reads of the same transcript were clustered, and redundant reads were removed to obtain consensus reads using the ICE algorithm. - The number of mapped reads in the 18 libraries ranged from to and the mapping ratios ranged from 77.55 to 85.16 % (Supplementary Table S1).. - To investigate the global differences in the transcrip- tome dynamics between the albino mutants and green seedlings, we identified 1,903 (AhWr vs. - However, the expression patterns of the 877 genes in cluster 5 were unusual: they were not expressed in AhWf, AhWs, or AhWr but were strongly expressed in AhCf, AhCs, and AhCr (Fig. - KEGG enrichment analysis of the SCMs showed that the top three enriched KEGG pathways were ‘protein digestion and absorption’, ‘biosynthesis of phenylpropanoids’, Table 2 Summary of RNA-seq data for all samples. - Further analysis showed that 76 SCMs in the albino mutants were associated with metabolic pathways, and four were involved in the ‘carbon fixation in photosyn- thesis’ and ‘tricarboxylic acid cycle (TCA cycle)’ path- ways (Supplementary Table S4). - Network analysis of DEGs and SCMs related to carbon fixation and the TCA cycle in albino mutants. - To investigate the gene regulatory networks in the albino mutants, we identified co-expressed genes via WGCNA [18]. - Interest- ing pathways were also identified in the blue, magenta, and turquoise modules by GO and KEGG enrichment analysis.. - GO enrichment analysis of genes in the blue module showed that the ‘photosynthesis’ and ‘photosynthesis light reaction’ terms were significantly enriched (Fig. - Add- itionally, the ‘photosynthesis’ and ‘carbon fixation in photo- synthetic organisms’ pathways were significantly enriched in the blue module (Fig. - The genes in the magenta module were associated with the photosynthesis process and significantly enriched in the ‘photosynthesis’ pathway (Fig. - The ‘glycolysis/gluconeogenesis’ pathway was sig- nificantly enriched by KEGG enrichment analysis of genes in the turquoise module (Fig. - 2 Analysis of significantly changed metabolites. - We identified six DEGs involved in carbon fixation in the photosyn- thesis pathway. - 1 (MDH1), NADP-dependent malic enzyme (MAOX), NAD-dependent malic enzyme (MAOM), and NAD- dependent malic enzyme 2 (NAD-ME2) were downregu- lated in the albino seedlings. - These results sug- gest that the DEGs and SCMs related to carbon fixation in the photosynthetic pathway in the albino mutants jointly inhibit carbon fixation in response to albinism.. - Two genes and four metabolites were found to be related to the TCA cycle in the al- bino mutants. - 4 GO and KEGG enrichment analysis of genes. - GO analysis of genes in the blue module (A). - KEGG pathway enrichment analysis of genes in the blue (B), magenta (C), and turquoise (D) modules. - in the albino mutants. - 0.05) in the roots, stems, and leaves of the albino mutants, respectively, compared to green seedlings. - We compared the expression patterns of the differentially expressed TF genes and genes involved in metabolic pathways by Pearson correlation analysis and constructed a correlation network to assess possible co-expression or co- regulation patterns in response to plant albinism (Fig. - The most highly represented TF families in the correlation network corresponded to the MYB-related, bHLH, C2C2-CO-like, and HB-BELL TF families. - The bHLH TF gene UNE10 and the MYB-related TF gene RVE8 were identified as the hub genes in the TF-metabolic pathway gene correlation network. - UNE10 and RVE8 were downregulated in the al- bino mutants, which correlated with the downregulation of the majority of metabolic pathway genes, implying that UNE10 and RVE8 positively regulate genes related to car- bon fixation and energy metabolism.. - The expression patterns of most genes in the albino and green seedlings showed similar trends between the high-throughput sequencing data and qRT-PCR data. - In addition, the results of the correlation between qRT-PCR. - These results confirm the reliability of the gene expression values gener- ated from the sequencing data.. - By contrast, SMRT sequencing produces full-length tran- scripts, which greatly improves the accuracy of the se- quencing results [23–26]. - In addition, the short reads obtained from Illumina sequencing could be used to cor- rect the long reads obtained from SMRT sequencing to compensate for the insufficient sensitivity of SMRT se- quencing for detecting short sequences, as well as inser- tion and deletion errors, to further ensure the reliability of the sequencing results [27]. - This greatly improved the accuracy and depth of the study.. - Most of these studies have focused on the causes of albinism in the mutants [28, 29], whereas few studies have explored the effects after plant albinism, such as gene expression and metabolite changes. - A thorough analysis of the changes in gene expression and metabo- lites after plant albinism could improve the understand- ing of albino mutants. - In this study, 8,202 DEGs were identified as responding to albinism in three different tissues, and 298 SCMs were identified in the leaves of A.. - heterophyllus albino mutants. - Through GO and KEGG enrichment analysis of the genes in each module, we found that genes in the blue, turquoise, and magenta modules were significantly. - We also found that L-aspartic acid, citric acid, succinic acid, and fu- maric acid levels significantly increased in the albino mutants. - Further research on these DEGs and SCMs should shed light on the relationship between genes and metabolites and help identify the genes and metabolites that function in the plant response to albinism.. - Among the many environmental factors that influence plant development, light is one of the most critical [32]. - 7 qRT-PCR of the expression levels of eighteen DEGs in the roots, stems, and leaves of albino and green seedlings. - Plants use the CO 2 produced by self-respiration and CO 2 in the atmosphere for carbon fixation to synthesize the carbohydrates needed for growth and development [38, 39]. - In this study, L-aspartic acid was significantly upregulated and eight genes in the carbon fixation path- way were identified as differentially expressed in the albino mutant. - In this study, these three genes were downregulated more than 4-fold, and NAD-ME2 was downregulated more than 256-fold in the albino mutants compared to green A.. - Perhaps the release of CO 2 is inhibited in these mutants due to the downregulation of the candidate genes.. - In summary, we propose that during carbon fixation, the efficiency of CO 2 fixation and CO 2 release are inhib- ited in the albino mutants, suggesting that insufficient materials are produced for plant growth and develop- ment. - This might be the cause of the premature death of A. - The TCA cycle plays a crucial role in cell energy metab- olism and ensures the supply of the materials and energy needed for the growth and development of organisms [47]. - In this study, the DEGs involved in the TCA cycle were all downregulated, and ACO1 was downregulated. - more than 512-fold in the albino mutants compared to green seedlings. - Therefore, we propose that the downregulation of ACO1 is a key factor in the dwarf phenotype of the A. - ACO1 encodes aconiticase 1, the first enzyme involved in the TCA cycle, which catalyzes the conversion of citric acid to cis-aconitic acid. - These findings suggest that the downregulation of ACO1 inhibits the conversion of citric acid to cis- aconitic acid, thereby disrupting the TCA cycle and inhi- biting energy production in the albino mutants.. - Moreover, 298 SCMs were detected in the leaves using UPLC-MS/MS.. - heterophyllus seedling albinism, lay- ing the foundation for further analysis of the regulatory mechanisms of carbon fixation and the TCA cycle. - We accidentally discovered the albino mutants in the offspring of an A. - The roots, stems, and leaves of the seedlings were used for analysis. - The leaves and stems of the A. - The quality of the 18 RNA samples was assessed using a NanoDrop 2000 (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). - The double-stranded cDNA was purified using AMPure XP beads and subjected to end repair, the addition of the poly-A tail, ligation of the sequencing linker, and fragment size selection. - We removed the unligated linker sequences at both ends of the cDNA, added primers, and used DNA polymerase to form a complete SMRTbell library.. - In jackfruit albino seedlings, the first and most obvious part of the albino phenomenon is the leaves (Supple- mentary Fig. - All DEGs were mapped to individual terms in the Gene Ontology (GO) database (http://www.. - GO enrichment analysis was then per- formed using GOseq software to identify significantly enriched terms in the DEGs. - Eighteen DEGs in the roots, stems, and leaves of green and albino A. - The expres- sion levels of the DEGs were calculated using the 2 −△△Ct method against internal control gene [58]. - GO enrichment analysis of genes in six clusters. - GO enrichment analysis of cluster 1 (A), cluster 2 (B), cluster 3 (C), cluster 4 (D), cluster 5 (E), and cluster 6 (F).. - KEGG pathway analysis of genes in six clusters. - heterophyllus albino mutants and green seedlings.. - We thank the people in the School of Forestry, Hainan University who helped us find the mutant plants.. - The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive [59] in BIG Data Center (BIG Data Center Members 2019), Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, under accession numbers CRA002905 and CRA003273, which are publicly accessible at https://bigd.big.ac.cn/gsa.. - Integrated analyses of the transcriptome and metabolome of the leaves of albino tea cultivars reveal coordinated regulation of the carbon and nitrogen metabolism. - Comparative analysis of the metabolome and transcriptome between green and albino zones of variegated leaves from Hydrangea macrophylla ‘ Maculata ’ infected by hydrangea ringspot virus. - Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation. - Metabolomics Integrated with Transcriptomics Reveals Redirection of the Phenylpropanoids Metabolic Flux in Ginkgo biloba. - Characterization of the human ESC transcriptome by hybrid sequencing. - A single-molecule long-read survey of the human transcriptome. - Integrated analysis of the transcriptome and metabolome in young and mature leaves of Ginkgo biloba L. - The activities of the E3 ubiquitin ligase COP1/SPA, a key repressor in light signaling. - Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. - Gene and genome duplications and the origin of C4 photosynthesis: Birth of a trait in the Cleomaceae. - Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-sEq. - A global survey of the transcriptome of allopolyploid Brassica napus based on single-molecule long-read isoform sequencing and Illumina-based RNA sequencing data. - The developmental dynamics of the Populus stem transcriptome. - Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing
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