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Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis.

Miao Y, Zhu Z, Guo Q, Zhu Y, Yang X, Sun Y - Front Plant Sci (2016)

Bottom Line: A functional annotation analysis based on sequence similarity queries of the GO, COG, KEGG databases showed that these DEGs were mainly involved in many physiological and biochemical processes, such as material and energy metabolism, hormone signaling, cell growth, and transcription regulation.In addition, quantitative real-time PCR analysis revealed that the expression patterns of the DEGs were consistent with the transcriptome data, which further supported a role for the DEGs in stolon formation.This study provides novel resources for future genetic and molecular studies in T. edulis.

View Article: PubMed Central - PubMed

Affiliation: Institute of Chinese Medicinal Materials, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Tulipa edulis (Miq.) Baker is an important medicinal plant with a variety of anti-cancer properties. The stolon is one of the main asexual reproductive organs of T. edulis and possesses a unique morphology. To explore the molecular mechanism of stolon formation, we performed an RNA-seq analysis of the transcriptomes of stolons at three developmental stages. In the present study, 15.49 Gb of raw data were generated and assembled into 74,006 unigenes, and a total of 2,811 simple sequence repeats were detected in T. edulis. Among the three libraries of stolons at different developmental stages, there were 5,119 differentially expressed genes (DEGs). A functional annotation analysis based on sequence similarity queries of the GO, COG, KEGG databases showed that these DEGs were mainly involved in many physiological and biochemical processes, such as material and energy metabolism, hormone signaling, cell growth, and transcription regulation. In addition, quantitative real-time PCR analysis revealed that the expression patterns of the DEGs were consistent with the transcriptome data, which further supported a role for the DEGs in stolon formation. This study provides novel resources for future genetic and molecular studies in T. edulis.

No MeSH data available.


Related in: MedlinePlus

Clusters of orthologous groups classification of DEGs among different comparisons (control/experiment: T1/T2, T1/T3, and T2/T3) during T. edulis stolon formation. T1, T2, and T3 indicate the initial, middle and later periods of stolon formation, respectively.
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Figure 8: Clusters of orthologous groups classification of DEGs among different comparisons (control/experiment: T1/T2, T1/T3, and T2/T3) during T. edulis stolon formation. T1, T2, and T3 indicate the initial, middle and later periods of stolon formation, respectively.

Mentions: According to the COG database, the DEGs were functionally clustered into 22 classifications (Figure 8). The first three classifications in T1/T2 and T1/T3 comparisons were “general function prediction only,” “carbohydrate transport and metabolism,” and “amino acid transport and metabolism,” while “general function prediction only,” “carbohydrate transport and metabolism,” and “secondary metabolites biosynthesis, transport and catabolism” were the groups with the most DEGs in T2/T3 comparison. Moreover, the proportions of DEGs in T2/T3 comparison in “signal transduction mechanisms,” “posttranslational modification, protein turnover, chaperones,” “secondary metabolites biosynthesis, transport and catabolism” were higher than T1/T2 and T1/T3 comparisons, suggesting that these genes are important in later developmental stage.


Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis.

Miao Y, Zhu Z, Guo Q, Zhu Y, Yang X, Sun Y - Front Plant Sci (2016)

Clusters of orthologous groups classification of DEGs among different comparisons (control/experiment: T1/T2, T1/T3, and T2/T3) during T. edulis stolon formation. T1, T2, and T3 indicate the initial, middle and later periods of stolon formation, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814499&req=5

Figure 8: Clusters of orthologous groups classification of DEGs among different comparisons (control/experiment: T1/T2, T1/T3, and T2/T3) during T. edulis stolon formation. T1, T2, and T3 indicate the initial, middle and later periods of stolon formation, respectively.
Mentions: According to the COG database, the DEGs were functionally clustered into 22 classifications (Figure 8). The first three classifications in T1/T2 and T1/T3 comparisons were “general function prediction only,” “carbohydrate transport and metabolism,” and “amino acid transport and metabolism,” while “general function prediction only,” “carbohydrate transport and metabolism,” and “secondary metabolites biosynthesis, transport and catabolism” were the groups with the most DEGs in T2/T3 comparison. Moreover, the proportions of DEGs in T2/T3 comparison in “signal transduction mechanisms,” “posttranslational modification, protein turnover, chaperones,” “secondary metabolites biosynthesis, transport and catabolism” were higher than T1/T2 and T1/T3 comparisons, suggesting that these genes are important in later developmental stage.

Bottom Line: A functional annotation analysis based on sequence similarity queries of the GO, COG, KEGG databases showed that these DEGs were mainly involved in many physiological and biochemical processes, such as material and energy metabolism, hormone signaling, cell growth, and transcription regulation.In addition, quantitative real-time PCR analysis revealed that the expression patterns of the DEGs were consistent with the transcriptome data, which further supported a role for the DEGs in stolon formation.This study provides novel resources for future genetic and molecular studies in T. edulis.

View Article: PubMed Central - PubMed

Affiliation: Institute of Chinese Medicinal Materials, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Tulipa edulis (Miq.) Baker is an important medicinal plant with a variety of anti-cancer properties. The stolon is one of the main asexual reproductive organs of T. edulis and possesses a unique morphology. To explore the molecular mechanism of stolon formation, we performed an RNA-seq analysis of the transcriptomes of stolons at three developmental stages. In the present study, 15.49 Gb of raw data were generated and assembled into 74,006 unigenes, and a total of 2,811 simple sequence repeats were detected in T. edulis. Among the three libraries of stolons at different developmental stages, there were 5,119 differentially expressed genes (DEGs). A functional annotation analysis based on sequence similarity queries of the GO, COG, KEGG databases showed that these DEGs were mainly involved in many physiological and biochemical processes, such as material and energy metabolism, hormone signaling, cell growth, and transcription regulation. In addition, quantitative real-time PCR analysis revealed that the expression patterns of the DEGs were consistent with the transcriptome data, which further supported a role for the DEGs in stolon formation. This study provides novel resources for future genetic and molecular studies in T. edulis.

No MeSH data available.


Related in: MedlinePlus