Limits...
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 DEGs in 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. (A) Venn diagram representing the unique and common DEGs among different comparisons. (B) The expression patterns of DEGs among different comparisons.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: The DEGs in 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. (A) Venn diagram representing the unique and common DEGs among different comparisons. (B) The expression patterns of DEGs among different comparisons.

Mentions: Using EBSeq software, 5,119 DEGs were detected in at least one comparison sample (control/experiment: T1/T2, T1/T3, and T2/T3). A Venn diagram was constructed to represent the numbers of DEGs in two or more comparisons (Figure 5A). Among the three comparisons, T2/T3 contained the smallest number of DEGs (1,747), whereas 2,856 and 3,445 DEGs were detected in T1/T2 and T1/T3, respectively. Of these, 164 DEGs was specifically detected in all comparisons. This result indicated that gene differences in the initial stage of development were the greatest. Gene transcript abundance was further analyzed as shown in Figure 5B. Compared with T1, 1,383 and 1,709 genes were up-regulated, and 1,473 and 1,736 genes were down-regulated in T2 and T3, respectively. While in T2/T3, 902 genes were up-regulated and 845 genes were down-regulated. Transcript abundances of all unigenes in stolon in different stages of T. edulis were measured by RPKM (Mortazavi et al., 2008). The RPKM values were first evaluated to check the distributions in three samples (Supplementary Figure S3). The transcript abundances of all unigenes were clustered using hierarchical cluster analysis (Figure 6). Based on the expression analysis, we also found that T1 had a large difference compared to T2 and T3, while a similar pattern was observed between T2 and T3.


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 DEGs in 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. (A) Venn diagram representing the unique and common DEGs among different comparisons. (B) The expression patterns of DEGs among different comparisons.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: The DEGs in 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. (A) Venn diagram representing the unique and common DEGs among different comparisons. (B) The expression patterns of DEGs among different comparisons.
Mentions: Using EBSeq software, 5,119 DEGs were detected in at least one comparison sample (control/experiment: T1/T2, T1/T3, and T2/T3). A Venn diagram was constructed to represent the numbers of DEGs in two or more comparisons (Figure 5A). Among the three comparisons, T2/T3 contained the smallest number of DEGs (1,747), whereas 2,856 and 3,445 DEGs were detected in T1/T2 and T1/T3, respectively. Of these, 164 DEGs was specifically detected in all comparisons. This result indicated that gene differences in the initial stage of development were the greatest. Gene transcript abundance was further analyzed as shown in Figure 5B. Compared with T1, 1,383 and 1,709 genes were up-regulated, and 1,473 and 1,736 genes were down-regulated in T2 and T3, respectively. While in T2/T3, 902 genes were up-regulated and 845 genes were down-regulated. Transcript abundances of all unigenes in stolon in different stages of T. edulis were measured by RPKM (Mortazavi et al., 2008). The RPKM values were first evaluated to check the distributions in three samples (Supplementary Figure S3). The transcript abundances of all unigenes were clustered using hierarchical cluster analysis (Figure 6). Based on the expression analysis, we also found that T1 had a large difference compared to T2 and T3, while a similar pattern was observed between T2 and T3.

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