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Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation.

Firon N, LaBonte D, Villordon A, Kfir Y, Solis J, Lapis E, Perlman TS, Doron-Faigenboim A, Hetzroni A, Althan L, Adani Nadir L - BMC Genomics (2013)

Bottom Line: The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database.A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change).This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel. vcfiron@volcani.agri.gov.il

ABSTRACT

Background: The number of fibrous roots that develop into storage roots determines sweetpotato yield. The aim of the present study was to identify the molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) generating a database for the sweetpotato root transcriptome using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous and initiating storage roots; (2) comparing the expression profiles of initiating storage roots and fibrous roots, using the Illumina Genome Analyzer to sequence cDNA libraries of the two root types and map the data onto the root transcriptome database.

Results: Use of the 454-Roche platform generated a total of 524,607 reads, 85.6% of which were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database. A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change). The Illumina-based differential expression results were validated for nine putative genes using quantitative real-time PCR. The differential expression profiles indicated down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots, and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, data indicated delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation.

Conclusions: This study adds a valuable resource of sweetpotato root transcript sequences to available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel transcripts related to storage root initiation identified in this study provide a starting point for further investigation into the molecular mechanisms underlying this process.

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GO-term enrichment in the fibrous root sample (‘sample’) relative to the root transcriptome database (‘reference’). Fibrous root sample histograms are indicated in black, while the ‘reference’ histograms are indicated in yellow. A. Biological process (BP). B. GO terms included in the ‘Secondary metabolic process’ BP category. C. Molecular function (MF) and cellular component (CC) categories.
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Figure 10: GO-term enrichment in the fibrous root sample (‘sample’) relative to the root transcriptome database (‘reference’). Fibrous root sample histograms are indicated in black, while the ‘reference’ histograms are indicated in yellow. A. Biological process (BP). B. GO terms included in the ‘Secondary metabolic process’ BP category. C. Molecular function (MF) and cellular component (CC) categories.

Mentions: The up-regulated contigs in FRs were found to represent a larger number of different enriched GO functional categories (FDR ≤ 0.05) compared to ISRs (Figure 10 and Additional files 9 and 10). Among the enriched terms represented by the up-regulated contigs in FRs, a total of 74 terms were included in the BP category, containing the ‘level 2’ terms “oxidation reduction” (GO:0055114), “small molecule metabolic process” (GO:0044281), “response to stress” (GO:0006950), “response to biotic stimulus” (GO:0009607), “response to chemical stimulus” (GO:0042221) and “secondary metabolic process” (GO:0019748), and the ‘level 3’ terms “response to endogenous stimulus” (GO: GO:0009719) and “transport” (GO:0006810), which in turn included “transmembrane transport” (GO:0055085). The enriched “secondary metabolic process” term exhibited high enrichment in “phenylpropanoid metabolic process” (GO:0009698; containing several contigs of coumaroyl CoA synthase and phenylalanine ammonia lyase), “phenylpropanoid biosynthetic process” (GO:0009699), “coumarin metabolic process” (GO:0009804), “coumarin biosynthetic process” (GO:0009805; containing contigs of p-coumaroyl quinate/shikimate 3′-hydroxylase, caffeoyl coenzyme A 3-o-methtyl transferase), “lignin metabolic process” (GO:0009808), “phenylpropanoid catabolic process” (GO:0046271 see Figure 10) and “lignin catabolic process” (GO:0046274). An interesting group of enriched functional terms (FDR ≤ 0.032) included: “meristem determinacy” (GO:0010022), “meristem maintenance” (GO:0010073) and “inflorescence meristem growth” (GO:0010450), which contained several contigs representing at least three ultrapetala 1-like proteins. Ultrapetala 1-like protein is a putative transcription factor that acts as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems [45]. The higher-plant shoot apical meristem is a dynamic structure that continuously produces cells which become incorporated into new leaves, stems and flowers. The maintenance of a constant flow of cells through the meristem depends on coordination of two antagonistic processes: self-renewal of the stem cell population and initiation of the lateral organs. This coordination is stringently controlled by gene networks that contain both positive and negative components. Carles et al. [45,46] defined the ULTRAPETALA1 (ULT1) gene as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems, because mutations in ULT1 caused enlargement of inflorescence and floral meristems, the production of supernumerary flowers and floral organs, and a delay in floral meristem termination.


Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation.

Firon N, LaBonte D, Villordon A, Kfir Y, Solis J, Lapis E, Perlman TS, Doron-Faigenboim A, Hetzroni A, Althan L, Adani Nadir L - BMC Genomics (2013)

GO-term enrichment in the fibrous root sample (‘sample’) relative to the root transcriptome database (‘reference’). Fibrous root sample histograms are indicated in black, while the ‘reference’ histograms are indicated in yellow. A. Biological process (BP). B. GO terms included in the ‘Secondary metabolic process’ BP category. C. Molecular function (MF) and cellular component (CC) categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3716973&req=5

Figure 10: GO-term enrichment in the fibrous root sample (‘sample’) relative to the root transcriptome database (‘reference’). Fibrous root sample histograms are indicated in black, while the ‘reference’ histograms are indicated in yellow. A. Biological process (BP). B. GO terms included in the ‘Secondary metabolic process’ BP category. C. Molecular function (MF) and cellular component (CC) categories.
Mentions: The up-regulated contigs in FRs were found to represent a larger number of different enriched GO functional categories (FDR ≤ 0.05) compared to ISRs (Figure 10 and Additional files 9 and 10). Among the enriched terms represented by the up-regulated contigs in FRs, a total of 74 terms were included in the BP category, containing the ‘level 2’ terms “oxidation reduction” (GO:0055114), “small molecule metabolic process” (GO:0044281), “response to stress” (GO:0006950), “response to biotic stimulus” (GO:0009607), “response to chemical stimulus” (GO:0042221) and “secondary metabolic process” (GO:0019748), and the ‘level 3’ terms “response to endogenous stimulus” (GO: GO:0009719) and “transport” (GO:0006810), which in turn included “transmembrane transport” (GO:0055085). The enriched “secondary metabolic process” term exhibited high enrichment in “phenylpropanoid metabolic process” (GO:0009698; containing several contigs of coumaroyl CoA synthase and phenylalanine ammonia lyase), “phenylpropanoid biosynthetic process” (GO:0009699), “coumarin metabolic process” (GO:0009804), “coumarin biosynthetic process” (GO:0009805; containing contigs of p-coumaroyl quinate/shikimate 3′-hydroxylase, caffeoyl coenzyme A 3-o-methtyl transferase), “lignin metabolic process” (GO:0009808), “phenylpropanoid catabolic process” (GO:0046271 see Figure 10) and “lignin catabolic process” (GO:0046274). An interesting group of enriched functional terms (FDR ≤ 0.032) included: “meristem determinacy” (GO:0010022), “meristem maintenance” (GO:0010073) and “inflorescence meristem growth” (GO:0010450), which contained several contigs representing at least three ultrapetala 1-like proteins. Ultrapetala 1-like protein is a putative transcription factor that acts as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems [45]. The higher-plant shoot apical meristem is a dynamic structure that continuously produces cells which become incorporated into new leaves, stems and flowers. The maintenance of a constant flow of cells through the meristem depends on coordination of two antagonistic processes: self-renewal of the stem cell population and initiation of the lateral organs. This coordination is stringently controlled by gene networks that contain both positive and negative components. Carles et al. [45,46] defined the ULTRAPETALA1 (ULT1) gene as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems, because mutations in ULT1 caused enlargement of inflorescence and floral meristems, the production of supernumerary flowers and floral organs, and a delay in floral meristem termination.

Bottom Line: The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database.A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change).This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel. vcfiron@volcani.agri.gov.il

ABSTRACT

Background: The number of fibrous roots that develop into storage roots determines sweetpotato yield. The aim of the present study was to identify the molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) generating a database for the sweetpotato root transcriptome using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous and initiating storage roots; (2) comparing the expression profiles of initiating storage roots and fibrous roots, using the Illumina Genome Analyzer to sequence cDNA libraries of the two root types and map the data onto the root transcriptome database.

Results: Use of the 454-Roche platform generated a total of 524,607 reads, 85.6% of which were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database. A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change). The Illumina-based differential expression results were validated for nine putative genes using quantitative real-time PCR. The differential expression profiles indicated down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots, and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, data indicated delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation.

Conclusions: This study adds a valuable resource of sweetpotato root transcript sequences to available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel transcripts related to storage root initiation identified in this study provide a starting point for further investigation into the molecular mechanisms underlying this process.

Show MeSH
Related in: MedlinePlus