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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

Heatmap clustering and qRT-PCR analysis of DEGs in T. edulis stolon formation. T1, T2 and T3 indicate the initial, middle and later periods of stolon formation, respectively. (A) The DEGs related to cell growth. (1) Transcript abundances of DEGs. (2) Relative expression levels of DEGs. (B) The DEGs related to hormone signal. (C) The DEGs related to sugar metabolism. (D) The DEGs related to sugar synthesis. (E) The DEGs related to amino acid metabolism. RPKM values were log2-based. The qRT-PCR data are presented as the mean ± SD of three biological and technical replicates.
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Figure 10: Heatmap clustering and qRT-PCR analysis of DEGs in T. edulis stolon formation. T1, T2 and T3 indicate the initial, middle and later periods of stolon formation, respectively. (A) The DEGs related to cell growth. (1) Transcript abundances of DEGs. (2) Relative expression levels of DEGs. (B) The DEGs related to hormone signal. (C) The DEGs related to sugar metabolism. (D) The DEGs related to sugar synthesis. (E) The DEGs related to amino acid metabolism. RPKM values were log2-based. The qRT-PCR data are presented as the mean ± SD of three biological and technical replicates.

Mentions: The results of function annotation suggested that a large number of DEGs associated with stolon formation. In this study, we selected genes for qRT-PCR validation. These genes were predicted to be related to cell growth (Te63130, Te97586, Te97174, Te85890), hormone signaling (Te93471, Te85890, Te88793, Te94375), sugar metabolism (Te76663, Te99064, Te81963, Te96901, Te80628), sugar synthesis (Te98020, Te98020-2, Te84600, Te89964), and amino acid metabolism (Te83464, Te91383, Te95795). The gene annotations of these DEGs are represented in Supplementary Table S2. At the same time, the transcript abundances of these DEGs are calculated with log2 ‘relative RPKM.’ According to the results (Figure 10), the qRT-PCR analysis and transcriptome data of most genes were consistent.


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)

Heatmap clustering and qRT-PCR analysis of DEGs in T. edulis stolon formation. T1, T2 and T3 indicate the initial, middle and later periods of stolon formation, respectively. (A) The DEGs related to cell growth. (1) Transcript abundances of DEGs. (2) Relative expression levels of DEGs. (B) The DEGs related to hormone signal. (C) The DEGs related to sugar metabolism. (D) The DEGs related to sugar synthesis. (E) The DEGs related to amino acid metabolism. RPKM values were log2-based. The qRT-PCR data are presented as the mean ± SD of three biological and technical replicates.
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Related In: Results  -  Collection

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Figure 10: Heatmap clustering and qRT-PCR analysis of DEGs in T. edulis stolon formation. T1, T2 and T3 indicate the initial, middle and later periods of stolon formation, respectively. (A) The DEGs related to cell growth. (1) Transcript abundances of DEGs. (2) Relative expression levels of DEGs. (B) The DEGs related to hormone signal. (C) The DEGs related to sugar metabolism. (D) The DEGs related to sugar synthesis. (E) The DEGs related to amino acid metabolism. RPKM values were log2-based. The qRT-PCR data are presented as the mean ± SD of three biological and technical replicates.
Mentions: The results of function annotation suggested that a large number of DEGs associated with stolon formation. In this study, we selected genes for qRT-PCR validation. These genes were predicted to be related to cell growth (Te63130, Te97586, Te97174, Te85890), hormone signaling (Te93471, Te85890, Te88793, Te94375), sugar metabolism (Te76663, Te99064, Te81963, Te96901, Te80628), sugar synthesis (Te98020, Te98020-2, Te84600, Te89964), and amino acid metabolism (Te83464, Te91383, Te95795). The gene annotations of these DEGs are represented in Supplementary Table S2. At the same time, the transcript abundances of these DEGs are calculated with log2 ‘relative RPKM.’ According to the results (Figure 10), the qRT-PCR analysis and transcriptome data of most genes were consistent.

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