Reconstruction of Starch Biosynthesis Pathway in Cassava Using Comparative Genomic Approach

Rongsirikul, Oratai; Saithong, Treenut; Kalapanulak, Saowalak; Meechai, Asawin; Cheevadhanarak, Supapon; Netrphan, Supatcharee; Suksangpanomrung, Malinee

doi:10.1007/978-3-642-16750-8_11

Cited by 3 publications

(7 citation statements)

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“…Due to the lack of a metabolic gap, we are claiming that the starch biosynthesis pathway of cassava was successfully reconstructed from the 270 cassava proteins identified by these five template plants. Compared to the two previous pathways proposed by Sakurai et al (2007) and Rongsirikul et al (2010), our reconstructed pathway definitely provides more complete information on the process underlying the starch biosynthesis in cassava [ 6 , 21 ].…”

Section: Resultsmentioning

confidence: 73%

“…The starch biosynthesis pathway, which covers three main processes including the Calvin cycle, sucrose synthesis, and storage starch biosynthesis, was reconstructed in this work. The reconstruction protocol was developed based on the similar basic idea as [ 21 ] in the exploitation of the multiple template plants for the pathway annotation, but it was re-designed to incorporate certain intensive analyses to ensure the high-level of quality of the resulting pathway. As outlined in Figure 1 , multiple plant species were employed to identify the set of starch-related genes in cassava.…”

Section: Resultsmentioning

confidence: 99%

“…The quality of the pathway here is not only defined by the parsimonious reconstruction framework, but also the visualization styles enhancing the pathway utilization for further research. With respect to the most recently proposed pathway of cassava starch biosynthesis [ 21 ], which contained less confident annotation with weak validation process, the contribution of this work provides a higher-quality pathway of starch biosynthesis in cassava.…”

Section: Resultsmentioning

confidence: 99%

“…Considering the starch biosynthesis pathway exemplified in their studies, it obviously showed an information deficiency containing several gaps in the resulting pathway. As a result, shortly after the availability of the cassava genome sequence in the Phytozome database, [ 21 ] revised such a pathway by using a more stringent comparative genomic protocol. The resulting pathway relatively contained more complete information, yet with further development, not only the quality of the reconstructed pathway would be improved, but the assurance for reliability and its further uses would also be confirmed.…”

Section: Introductionmentioning

confidence: 99%

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Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

et al. 2013

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BackgroundCassava is a well-known starchy root crop utilized for food, feed and biofuel production. However, the comprehension underlying the process of starch production in cassava is not yet available.ResultsIn this work, we exploited the recently released genome information and utilized the post-genomic approaches to reconstruct the metabolic pathway of starch biosynthesis in cassava using multiple plant templates. The quality of pathway reconstruction was assured by the employed parsimonious reconstruction framework and the collective validation steps. Our reconstructed pathway is presented in the form of an informative map, which describes all important information of the pathway, and an interactive map, which facilitates the integration of omics data into the metabolic pathway. Additionally, to demonstrate the advantage of the reconstructed pathways beyond just the schematic presentation, the pathway could be used for incorporating the gene expression data obtained from various developmental stages of cassava roots. Our results exhibited the distinct activities of the starch biosynthesis pathway in different stages of root development at the transcriptional level whereby the activity of the pathway is higher toward the development of mature storage roots.ConclusionsTo expand its applications, the interactive map of the reconstructed starch biosynthesis pathway is available for download at the SBI group’s website (http://sbi.pdti.kmutt.ac.th/?page_id=33). This work is considered a big step in the quantitative modeling pipeline aiming to investigate the dynamic regulation of starch biosynthesis in cassava roots.

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Section: Resultsmentioning

confidence: 73%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

et al. 2013

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“…The extended metabolic pathways are available in the Plant Metabolic Network (PMN) database (Schlapfer et al, 2017). Comparative genomics approach, in addition, has made it possible to evaluate the convergence and divergence of metabolic pathways in cassava and evolutionarily related plants, and has deepened our understanding of carbon assimilation in cassava (Rongsirikul et al, 2010;Saithong et al, 2013;Siriwat, 2012). Reconstruction of metabolic network merely based on metabolic components, i.e.…”

Section: Introductionmentioning

confidence: 99%

Development of a compartmentalized model for insight into the structured metabolic pathway of carbon metabolism in cassava leaves

2019

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In silico metabolic modeling has enabled systematic study of complicated metabolic processes underlying phenotypes of organisms. Modeling of plant metabolism is often hampered by the network complexity and lack of adequate knowledge. The existing metabolic networks of cassava only cover broad metabolism and are not compartmentalized to truly represent metabolism in photosynthetic tissues. To address the aforementioned limitations and develop a robust metabolic network, physiological and genomic data derived from cassava and leaf models of Arabidopsis and rice were to extend the scope of the existing model. The proposed compartmentalized network of metabolism in photosynthetic tissues of cassava, ph-MeRecon (photosynthetic-Manihot esculenta Metabolic Pathway Reconstruction) was developed based on the information resulting of the comparative study of multiple model plants and cassava genome. The ph-MeRecon covers primary carbon metabolism and comprises 461 metabolites, 550 reactions, and 1,037 metabolic genes. Enzymatic genes on the network were validated using RNA-expression data, and the reactions and pathways were compartmentalized into cytoplasm, chloroplast, mitochondria, and peroxisome. To ensure network connectivity, metabolic gaps were filled using gap reactions obtained from literature and metabolic pathway omnibus. In addition, information on plant physiology, including photosynthetic light-dependent reactions, carboxylase and oxygenase activity of RuBisCO enzyme, and phosphoenolpyruvate carboxylase enzyme activity was incorporated into ph-MeRecon to mimic cellular metabolism in cassava leaves. Thus, ph-MeRecon offers a multi-level platform for system analysis of cellular mechanisms underlying phenotypes of interest in cassava. The ph-MeRecon metabolic model is available at http://bml.sbi.kmutt.ac.th/ph-MeRecon/.

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Transcriptomic Data Integration Inferring the Dominance of Starch Biosynthesis in Carbon Utilization of Developing Cassava Roots

Siriwat

Kalapanulak

Suksangpanomrung

et al. 2012

Procedia Computer Science

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Reconstruction of Starch Biosynthesis Pathway in Cassava Using Comparative Genomic Approach

Cited by 3 publications

References 3 publications

Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration

Development of a compartmentalized model for insight into the structured metabolic pathway of carbon metabolism in cassava leaves

Transcriptomic Data Integration Inferring the Dominance of Starch Biosynthesis in Carbon Utilization of Developing Cassava Roots

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