scholarly journals Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Keisuke Suematsu ◽  
Masaru Tanaka ◽  
Rie Kurata ◽  
Yumi Kai
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Carotenoid Biosynthesis ◽  
Comparative Transcriptome ◽  
Storage Roots ◽  
Zeaxanthin Epoxidase ◽  
Carotenoid Accumulation ◽  
Carotenoid Composition ◽  
Yellow Flesh ◽  
Β Carotene

AbstractThe mechanisms of carotenoid accumulation in yellow-fleshed sweetpotato cultivars are unclear. In this study, we compared the transcriptome profiles of a yellow-fleshed cultivar, Beniharuka (BH) and two of its spontaneous white-fleshed mutants (WH2 and WH3) to reveal the genes involved in yellow flesh. As a result of RNA sequencing, a total of 185 differentially expressed genes (DEGs) were commonly detected in WH2 and WH3 compared to BH. Of these genes, 85 DEGs and 100 DEGs were commonly upregulated and downregulated in WH2 and WH3 compared to BH, respectively. g1103.t1, a paralog of zeaxanthin epoxidase (ZEP), was only DEG common to WH2 and WH3 among 38 genes considered to be involved in carotenoid biosynthesis in storage roots. The expression level of g1103.t1 was also considerably lower in five white-fleshed cultivars than in five yellow-fleshed cultivars. Analysis of carotenoid composition in the storage roots showed that the epoxidised carotenoids were drastically reduced in both WH2 and WH3. Therefore, we propose that the ZEP paralog, g1103.t1, may be involved in carotenoid accumulation through the epoxidation of β-carotene and β-cryptoxanthin in sweetpotato.

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

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiuling Li ◽  
Jizheng Fan ◽  
Shuming Luo ◽  
Ling Yin ◽  
Hongying Liao ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Color Variation ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Regulatory Pathways ◽  
Comparative Transcriptome Analysis ◽  
Color Formation ◽  
Carotenoid Accumulation

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.

scholarly journals Expression of Carotenoid Biosynthetic Genes and Carotenoid Biosynthesis during Seedling Development of Momordica charantia

2018 ◽  
Vol 13 (3) ◽  
pp. 1934578X1801300
Author(s):  
Do Manh Cuong ◽  
Jae Kwang Kim ◽  
Jin Jeon ◽  
Tae Jin Kim ◽  
Jong Seok Park ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carotenoid Biosynthesis ◽  
Seedling Development ◽  
Bitter Melon ◽  
Biosynthetic Genes ◽  
Carotenoid Concentration ◽  
Carotenoid Accumulation ◽  
Firm Basis ◽  
Phytohormone Synthesis ◽  
Β Carotene

Carotenoids belong to a large group of secondary metabolites, and have pivotal roles in plants, including photosynthesis and phytohormone synthesis, pigmentation, and membrane stabilization. Additionally, carotenoids are potent antioxidants, and their health benefits are becoming increasingly prominent. In recent years, carotenoids have been studied in many plants. Furthermore, gene expression, as well as carotenoid accumulation in different parts of the bitter melon, has been investigated; however, it has not been studied in bitter melon seedlings. In this study, carotenoid accumulation and transcript levels of McGGPPS1, McGGPPS2, McPSY, McPDS, McZDS, McLCYB, McLCYE1, McLCYE2, McCXHB, and McZEP, involved in carotenoid biosynthesis, were analyzed during seedling development using HPLC and qRT-PCR. The major carotenoids that accumulated in the bitter melon seedlings were lutein and E-β-carotene. The expression of most carotenoid biosynthetic genes increased during seedling development, consistent with the accumulation of violaxanthin, lutein, zeaxanthin, β-cryptoxanthin, 13Z-β-carotene, E-β-carotene, and 9Z-β-carotene in bitter melon seedlings. The results of this study provide a firm basis for comprehending the link between gene expression and carotenoid concentration in bitter melon seedlings.

scholarly journals Comparative transcriptome analysis of rumen papillae in suckling and weaned Japanese Black calves using RNA sequencing

2018 ◽  
Vol 96 (6) ◽  
pp. 2226-2237 ◽  
Author(s):  
Koki Nishihara ◽  
Daichi Kato ◽  
Yutaka Suzuki ◽  
Dahye Kim ◽  
Misato Nakano ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

scholarly journals Effects of Exogenous Abscisic Acid (ABA) on Carotenoids and Petal Color in Osmanthus fragrans ‘Yanhonggui’

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 454
Author(s):  
Yucheng Liu ◽  
Bin Dong ◽  
Chao Zhang ◽  
Liyuan Yang ◽  
Yiguang Wang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Metabolic Pathway ◽  
Carotenoid Biosynthesis ◽  
Carotenoid Content ◽  
Native Plant ◽  
Total Carotenoids ◽  
Osmanthus Fragrans ◽  
Carotenoid Accumulation ◽  
Β Carotene ◽  
Carotenoid Degradation

Osmanthus fragrans is a well-known native plant in China, and carotenoids are the main group of pigments in the petals. Abscisic acid (ABA) is one of the products of the metabolic pathway of carotenoids. Application of ABA could affect pigmentation of flower petals by changing the carotenoid content. However, little is known about the effects of ABA treatment on carotenoid accumulation in O. fragrans. In this study, different concentrations of ABA (0, 150 and 200 mg/L) were spread on the petals of O. fragrans ‘Yanhonggui’. The petal color of ‘Yanhonggui’ receiving every ABA treatment was deeper than that of the control. The content of total carotenoids in the petals significantly increased with 200 mg/L ABA treatment. In the petals, α-carotene and β-carotene were the predominant carotenoids. The expression of several genes involved in the metabolism of carotenoids increased with 200 mg/L ABA treatment, including PSY1, PDS1, Z-ISO1, ZDS1, CRTISO, NCED3 and CCD4. However, the transcription levels of the latter two carotenoid degradation-related genes were much lower than of the five former carotenoid biosynthesis-related genes; the finding would explain the significant increase in total carotenoids in ‘Yanhonggui’ petals receiving the 200 mg/L ABA treatment.

scholarly journals Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiangtao Yang ◽  
Lihua Gao ◽  
Xiaojing Liu ◽  
Xiaochun Zhang ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Fiber Development ◽  
Comparative Transcriptome

AbstractCotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

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