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


RESULTS
In 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.


CONCLUSIONS
To 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.
Bioinfromatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 10150 Bangkok, Thailand. treenut.sai@kmutt.ac.th.
Treenut
T
Saithong
Oratai
O
Rongsirikul
Saowalak
S
Kalapanulak
Porntip
P
Chiewchankaset
Wanatsanan
W
Siriwat
Supatcharee
S
Netrphan
Malinee
M
Suksangpanomrung
Asawin
A
Meechai
Supapon
S
Cheevadhanarak
D023281:Genomics / Q000379:methods*; D002365:Manihot / Q000235:genetics* / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D013213:Starch / Q000096:biosynthesis*; D059467:Transcriptome
D013213:Starch