Transcriptome analysis of rosette and folding leaves in Chinese cabbage using high-throughput RNA sequencing

Wang, Fengde; Li, Libin; Li, Huayin; Liu, Lifeng; Zhang, Yihui; Gao, Jianwei; Wang, Xiaowu

doi:10.1016/j.ygeno.2012.02.005

Cited by 44 publications

(56 citation statements)

References 46 publications

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“…Three replicates of each sample were conducted to calculate the average Ct values. The relative expression level was calculated by the comparative 2 −ΔΔCt method [35, 36]. The significance was determined with the SPSS software (SPSS 17.0, IBM, Chicago, IL, USA) ( p < 0.05).…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening

Wang

et al. 2016

International Journal of Genomics

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Anthocyanin in strawberries has a positive effect on fruit coloration. In this study, the role of exogenous hematin on anthocyanin biosynthesis was investigated. Our result showed that the white stage of strawberries treated with exogenous hematin had higher anthocyanin content, compared to the control group. Among all treatments, 5 μM of hematin was the optimal condition to promote color development. In order to explore the molecular mechanism of fruit coloring regulated by hematin, transcriptomes in the hematin- and non-hematin-treated fruit were analyzed. A large number of differentially expressed genes (DEGs) were identified in regulating anthocyanin synthesis, including the DEGs involved in anthocyanin biosynthesis, hormone signaling transduction, phytochrome signaling, starch and sucrose degradation, and transcriptional pathways. These regulatory networks may play an important role in regulating the color process of strawberries treated with hematin. In summary, exogenous hematin could promote fruit coloring by increasing anthocyanin content in the white stage of strawberries. Furthermore, transcriptome analysis suggests that hematin-promoted fruit coloring occurs through multiple related metabolic pathways, which provides valuable information for regulating fruit color via anthocyanin biosynthesis in strawberries.

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Section: Methodsmentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening

Wang

et al. 2016

International Journal of Genomics

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“…Based on these data and the results reported earlier [4], In this study, four libraries during lotus ARs formation in responding to sucrose were constructed to monitor metabolism change based on lotus seedlings develpmental feature. (Fig.1a, b) sequenced by solexa technology, which has been widely applied in exploring mechanism of plant growth and development [39][40]. we hypothesized that the plant hormone, IAA plays a crucial role during AR formation.…”

Section: The Role Of Iaa On the Formation Of Arsmentioning

confidence: 99%

Comparative transcriptome analysis revealed the cooperative regulation of sucrose and IAA on adventitious root formation in lotus (Nelumbo nucifera Gaertn)

Cheng

Minrong

Liu

et al. 2019

Preprint

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BackgroundIn China, lotus is an important cultivated crop with multiple applications in ornaments, food, and environmental purification. Adventitious roots (ARs), a secondary root is necessary for the uptake of nutrition and water as the lotus principle root is underdeveloped. To investigate the regulatory pathway during ARs formation, we analyzed the expression of genes and miRNAs upon treatment with differential concentrations of sucrose, and a crosstalk between sucrose and IAA was also identified. ResultsWe observed that the lotus ARs formation was significantly affected by sucrose treatment. Notably, 20 mg/L sucrose promoted the ARs development, whereas 60 mg/L sucrose inhibited the formation of ARs. The expression of genes and miRNAs was evaluated by high-throughput tag-sequencing. We observed that the expression of 5438, 5184, and 5345 genes was enhanced in the GL20/CK0, GL60/CK0, and CK1/CK0 libraries, respectively. Further, the expression of 73, 78, and 71 miRNAs was upregulated in the ZT20/MCK0, ZT60/MCK0, and MCK1/MCK0 libraries, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the differentially expressed genes and miRNAs in the GL20/GL60 and ZT20/ZT60 libraries were involved in signal transduction. A large number of these genes (29) and miRNAs (53) were associated with plant hormone metabolism. We observed an association between five miRNAs (miR160, miR156a-5p, miR397-5p_1, miR396a and miR167d) and nine genes (auxin response factor, protein brassinosteroid insensitive 1, laccase, and peroxidase 27) in the ZT20/ ZT60 libraries during ARs formation.Quantitative polymerase chain reaction (qPCR) was used to validate the high-throughput tagsequencing data. ConclusionsWe found that the expression of many critical genes involved in IAA synthesis and IAA transport was changed after treatment with various concentration of sucrose. Based on the change of these genes expression, IAA and sucrose content, we concluded that sucrose and IAA cooperatively regulated ARs formation. Sucrose affected ARs formation by improving IAA content at induction stage, and increased

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“…To analyze the expression pattern of these BrGRP genes in Chinese cabbage, the transcriptome data of B. rapa 'Chiifu' [43] and the inbred line 'Fushanbaotou', a typical heading Chinese cabbage [54] were downloaded and used for gene expression profiling in eight tissues including callus, root, stem, leaf, flower, silique, rosette and folding leaves.…”

Section: Expression Pattern Analysis Of Brgrp Genesmentioning

confidence: 99%

Genome-wide identification and expression analysis of glycine-rich protein genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Gao

Cheng

et al. 2019

Preprint

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Background Plant Glycine-rich proteins, a superfamily with a glycine-rich domain, play an important role in various stress such as low temperature, drought, high salt, and so on. Although the research of GRP genes has been reported in many plants, the GRP gene has seldom reported in Chinese cabbage so far. Research results made a guide to further understand the function of BrGRP genes in Chinese cabbage. Results In this study, a total of 141 glycine-rich protein genes were identified in Chinese cabbage by homology comparative analysis. A further prediction of physical and chemical characteristics revealed that 58.3% of BrGRPs were alkalines, 63.1% of BrGRPs were unstable, and 73.8% were hydrophilic. Conserved domain analysis showed that 110 BrGRPs contained 18 same conserved motifs, and could be classified into five main subclasses which the evolutionary relationship and gene structure may be conserved while the other 31 BrGRPs, including Bra014168 , Bra040002 , etc, may gain new functions or gradually lost gene functions according to the evolution process. These identified BrGRP genes were also located in ten chromosomes and three different subgenomes of Chinese cabbage, and 101 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the opened transcriptome data, we found that 138 BrGRP genes showed abnormal expression at high temperature, 108 BrGRP genes showed abnormal expression at low temperature, and 74 at drought stress, 47 at soft rot stress, while only 3 and 7 genes at ozone and salt stress, respectively. Further promoter motif analysis found that a large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE, were identified in their promoter regions, which were in correspondence with previous differential expression. In addition, some BrGRP genes were involved in multiple stresses suggested their broad-spectrum resistance. Conclusion A total of 141 GRP genes were identified in Chinese cabbage, which suggested their potential roles in plant stress response. But the molecular mechanisms by which BrGRP genes respond and resist biotic and abiotic stress remain unclear. These results may provide an important basis for the study of their function in Chinese cabbage.

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Transcriptome analysis of rosette and folding leaves in Chinese cabbage using high-throughput RNA sequencing

Cited by 44 publications

References 46 publications

Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening

Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening

Comparative transcriptome analysis revealed the cooperative regulation of sucrose and IAA on adventitious root formation in lotus (Nelumbo nucifera Gaertn)

Genome-wide identification and expression analysis of glycine-rich protein genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

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