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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

(A)Tulipa edulis with elongated stolon; (B)T. edulis stolon developed into a new bulb.
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Figure 1: (A)Tulipa edulis with elongated stolon; (B)T. edulis stolon developed into a new bulb.

Mentions: The stolon is one of the main asexual reproductive organs of T. edulis and possesses a unique morphology. The stolon is similar to the rhizome in appearance; however, the former has no visible node, internode, or adventitious root. The stolon begins at the stem, bulges outward and extends more than 10 cm at the bottom of the stem. Then, the stolon is pushed deeply in the soil or culture medium and develops a bulblet at the tip. Finally, the stolon shrivels up, and the bulblet, which is surrounded by a thin brown tunic remains (Figure 1; Custers et al., 1992; Miao et al., 2015). The stolon plus the bulblet together is called the dropper (Custers et al., 1992). In many studies, the formation of the stolon has been described in micropropagation culture in some Tulip spp. plants as a transition to bulblet formation (Custers et al., 1992; Koster, 1993). Nevertheless, there are few studies of the stolon in the tulip under natural conditions. In the tulip, stolon formation was observed in seedlings and small bulbs that grow in wet soil as well as in large bulbs (Le Nard and De Hertogh, 1993). The number of stolons significantly affects the reproductive index. In addition to being a reproductive organ, the stolon of T. edulis plays an important role in its adaptation to diverse conditions. Organ-specific gene expression contains rich information on in vivo biological processes. Organ differentiation in multi-cellular organisms depends on highly organized molecular events and lends enhanced functionalities to the organisms in their adaptation to natural environments (Guan and Lu, 2013). To date, only a few studies have described the structure of the stolon in similar plants (Custers et al., 1992; Koster, 1993), and research on the morphological characteristics and the development period of T. edulis stolon has not yet been performed. The poor understanding of the molecular mechanisms and regulatory networks limits the research on T. edulis stolon formation and further hampers the use of reliable technologies to improve the reproductive index of T. edulis. Therefore, it is necessary to explore gene networks and biological processes to promote the further study of stolon growth and to meet the strong market demand.


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)

(A)Tulipa edulis with elongated stolon; (B)T. edulis stolon developed into a new bulb.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4814499&req=5

Figure 1: (A)Tulipa edulis with elongated stolon; (B)T. edulis stolon developed into a new bulb.
Mentions: The stolon is one of the main asexual reproductive organs of T. edulis and possesses a unique morphology. The stolon is similar to the rhizome in appearance; however, the former has no visible node, internode, or adventitious root. The stolon begins at the stem, bulges outward and extends more than 10 cm at the bottom of the stem. Then, the stolon is pushed deeply in the soil or culture medium and develops a bulblet at the tip. Finally, the stolon shrivels up, and the bulblet, which is surrounded by a thin brown tunic remains (Figure 1; Custers et al., 1992; Miao et al., 2015). The stolon plus the bulblet together is called the dropper (Custers et al., 1992). In many studies, the formation of the stolon has been described in micropropagation culture in some Tulip spp. plants as a transition to bulblet formation (Custers et al., 1992; Koster, 1993). Nevertheless, there are few studies of the stolon in the tulip under natural conditions. In the tulip, stolon formation was observed in seedlings and small bulbs that grow in wet soil as well as in large bulbs (Le Nard and De Hertogh, 1993). The number of stolons significantly affects the reproductive index. In addition to being a reproductive organ, the stolon of T. edulis plays an important role in its adaptation to diverse conditions. Organ-specific gene expression contains rich information on in vivo biological processes. Organ differentiation in multi-cellular organisms depends on highly organized molecular events and lends enhanced functionalities to the organisms in their adaptation to natural environments (Guan and Lu, 2013). To date, only a few studies have described the structure of the stolon in similar plants (Custers et al., 1992; Koster, 1993), and research on the morphological characteristics and the development period of T. edulis stolon has not yet been performed. The poor understanding of the molecular mechanisms and regulatory networks limits the research on T. edulis stolon formation and further hampers the use of reliable technologies to improve the reproductive index of T. edulis. Therefore, it is necessary to explore gene networks and biological processes to promote the further study of stolon growth and to meet the strong market demand.

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