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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

The frequency of SSR motif types in T. edulis.
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Figure 4: The frequency of SSR motif types in T. edulis.

Mentions: Simple sequence repeats are widely used in genetic research, linkage map construction, and breeding study. To explore SSRs in T. edulis, 13,236 unigenes that had a length more than 1,000 bp were screened using MISA software. A total of 2,811 SSRs were identified in 2,484 unigenes, among which 280 unigenes had more than one SSR. The length of different SSR repeat types varied greatly (Table 3). The tri-nucleotide repeat type accounted for more than half (59.34%) of the total SSRs, followed by mono-nucleotide (27.89%) and di-nucleotide (11.95%). The remaining types (tetra-, penta-, hexa-) had a frequency of less than 1%. The frequencies of SSR motif types are shown in Figure 4. In mono-nucleotide repeats, the A/T type was the abundant type and accounted for 24.51%. The most frequent type of di-nucleotide repeats, AG/CT, accounted for the vast majority of the proportion and far more than the other three types. Among all motif types, CCG/CGG repeats represented the largest proportion (34.26%) of all motif types. Additionally, another tri-nucleotide motif, AGG/CCT, accounted for 10.85% of all SSRs. The formation of SSR repeat types with a higher G + C content showed an observable base preference.


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)

The frequency of SSR motif types in T. edulis.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: The frequency of SSR motif types in T. edulis.
Mentions: Simple sequence repeats are widely used in genetic research, linkage map construction, and breeding study. To explore SSRs in T. edulis, 13,236 unigenes that had a length more than 1,000 bp were screened using MISA software. A total of 2,811 SSRs were identified in 2,484 unigenes, among which 280 unigenes had more than one SSR. The length of different SSR repeat types varied greatly (Table 3). The tri-nucleotide repeat type accounted for more than half (59.34%) of the total SSRs, followed by mono-nucleotide (27.89%) and di-nucleotide (11.95%). The remaining types (tetra-, penta-, hexa-) had a frequency of less than 1%. The frequencies of SSR motif types are shown in Figure 4. In mono-nucleotide repeats, the A/T type was the abundant type and accounted for 24.51%. The most frequent type of di-nucleotide repeats, AG/CT, accounted for the vast majority of the proportion and far more than the other three types. Among all motif types, CCG/CGG repeats represented the largest proportion (34.26%) of all motif types. Additionally, another tri-nucleotide motif, AGG/CCT, accounted for 10.85% of all SSRs. The formation of SSR repeat types with a higher G + C content showed an observable base preference.

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