U.S. Department of EnergyOffice of Scientific and Technical Information
DNA parts and gene constructs for plant biodesign
Abstract
Plant biodesign requires the knowledge of DNA parts (e.g., genes, promoters, terminators), along with their combinations (as gene constructs) linked to engineered traits. DNA parts with validated or predicted functions in plants have been deposited in various online databases. However, these existing databases focus on basic biological functions of individual DNA parts, leaving a gap between basic knowledge and bioengineering applications. To fill this knowledge gap, we have created a user-friendly, open-ended database as a knowledge graph linking DNA parts to gene constructs to traits. This database contains experimentally validated DNA parts and gene constructs documented in peer-reviewed publications. The DNA parts include 1) molecular components with biological functions, such as genes involved in various biological processes (e.g., metabolic and signal transduction pathways) and 2) molecular components with technical functions, such as gene expression, genome engineering and sequence splicing. The gene constructs deposited in this database include both single-gene and multi-gene constructs. This database allows users to submit DNA parts and gene construct compositions linked to engineered traits described in peer-reviewed publications, providing a public digital repository for sharing the biodesign information among the researchers in the fields of plant biotechnology and plant synthetic biology.
- Authors:
-
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Center for Bioenergy Innovation
- Center for Bioenergy Innovation, Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA
- Publication Date:
- DOE Contract Number:
- AC05-00OR22725
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth & Environmental Systems Science (EESS)
- Subject:
- plant biodesign synthetic biology gene constructs DNA Parts
- OSTI Identifier:
- 2375785
- DOI:
- https://doi.org/10.25983/2375785
Citation Formats
Liu, Yang, Islam, Md Torikul, Rajput, Ruchika, Yao, Tao, Hopp, Dan, Martin, Stanton, Chen, Jin-Gui, Tsai, Chung-Jui, Abraham, Paul, Tschaplinski, Timothy, Tuskan, Gerald, and Yan, Xiaohan. DNA parts and gene constructs for plant biodesign. United States: N. p., 2024.
Web. doi:10.25983/2375785.
Liu, Yang, Islam, Md Torikul, Rajput, Ruchika, Yao, Tao, Hopp, Dan, Martin, Stanton, Chen, Jin-Gui, Tsai, Chung-Jui, Abraham, Paul, Tschaplinski, Timothy, Tuskan, Gerald, & Yan, Xiaohan. DNA parts and gene constructs for plant biodesign. United States. doi:https://doi.org/10.25983/2375785
Liu, Yang, Islam, Md Torikul, Rajput, Ruchika, Yao, Tao, Hopp, Dan, Martin, Stanton, Chen, Jin-Gui, Tsai, Chung-Jui, Abraham, Paul, Tschaplinski, Timothy, Tuskan, Gerald, and Yan, Xiaohan. 2024.
"DNA parts and gene constructs for plant biodesign". United States. doi:https://doi.org/10.25983/2375785. https://www.osti.gov/servlets/purl/2375785. Pub date:Thu Jun 20 00:00:00 EDT 2024
@article{osti_2375785,
title = {DNA parts and gene constructs for plant biodesign},
author = {Liu, Yang and Islam, Md Torikul and Rajput, Ruchika and Yao, Tao and Hopp, Dan and Martin, Stanton and Chen, Jin-Gui and Tsai, Chung-Jui and Abraham, Paul and Tschaplinski, Timothy and Tuskan, Gerald and Yan, Xiaohan},
abstractNote = {Plant biodesign requires the knowledge of DNA parts (e.g., genes, promoters, terminators), along with their combinations (as gene constructs) linked to engineered traits. DNA parts with validated or predicted functions in plants have been deposited in various online databases. However, these existing databases focus on basic biological functions of individual DNA parts, leaving a gap between basic knowledge and bioengineering applications. To fill this knowledge gap, we have created a user-friendly, open-ended database as a knowledge graph linking DNA parts to gene constructs to traits. This database contains experimentally validated DNA parts and gene constructs documented in peer-reviewed publications. The DNA parts include 1) molecular components with biological functions, such as genes involved in various biological processes (e.g., metabolic and signal transduction pathways) and 2) molecular components with technical functions, such as gene expression, genome engineering and sequence splicing. The gene constructs deposited in this database include both single-gene and multi-gene constructs. This database allows users to submit DNA parts and gene construct compositions linked to engineered traits described in peer-reviewed publications, providing a public digital repository for sharing the biodesign information among the researchers in the fields of plant biotechnology and plant synthetic biology.},
doi = {10.25983/2375785},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Jun 20 00:00:00 EDT 2024},
month = {Thu Jun 20 00:00:00 EDT 2024}
}