KIPEs3:生物合成途径的自动注释
Andreas Rempel1,2, Nancy Choudhary3, Boas Pucker3
1Genome Informatics, Faculty of Technology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
PloS one
|November 16, 2023
概括
KIPEs3是一个先进的工具,可以自动注释植物生物合成途径,包括黄类和胡卜素. 它有助于识别用于色素生产,修饰和运输的基因,支持进化和育种研究.
科学领域:
- 植物生物化学和分子生物学
- 生物信息学和计算生物学
背景情况:
- 黄和胡卜素是关键的植物颜料,参与着着色和应激反应.
- 它们的生物合成途径在很大程度上保持不变,但具有特定物种的修改.
研究的目的:
- 引入KIPEs3,一个改进的工具,用于植物生物合成途径的自动注释.
- 扩大KIPE的能力,包括黄和胡卜素生物合成,包括装饰和运输基因.
- 为了促进大规模基因组数据的分析,以获得进化和生物技术的见解.
主要方法:
- 开发和应用KIPEs3用于路径注释.
- 在Arabidopsis thaliana,Capsella grandiflora和Dioscorea dumetorum中对黄类生物合成的分析.
- 在Arabidopsis thaliana,Capsella grandiflora,Dioscorea dumetorum和Daucus carota中对胡卜素生物合成的分析.
主要成果:
- KIPEs3成功地确定了核心生物合成参与者以及黄类装饰和运输的候选者.
- 证明了该工具在多种植物物种中对黄类和胡卜素路径的适用性.
- 通过案例研究验证了KIPEs3的功能和易用性.
结论:
- KIPEs3是一个强大且易于访问的在线服务,用于高质量,大规模的植物生物合成途径分析.
- 该工具支持用于进化研究和育种应用的候选基因的识别.
- KIPEs3使得没有广泛生物信息学经验的研究人员能够分析复杂的植物基因组数据.
更多相关视频
相关概念视频
01:29Amino Acid Biosynthetic Pathways
17
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
17
01:24Biosynthesis in Bacteria
20
Biosynthesis in bacteria is a fundamental anabolic process that generates essential macromolecules, including proteins, nucleic acids, lipids, and polysaccharides. These macromolecules are critical for cellular growth, replication, and function. The process is tightly regulated and energetically linked to catabolic pathways to ensure optimal resource utilization.Biosynthetic pathways begin with precursor metabolites such as pyruvate, acetyl-CoA, and glucose-6-phosphate derived from glycolysis,...
20
03:36Genome Annotation and Assembly
18.9K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.9K
01:27C4 Pathway and CAM
45.6K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
C4 Pathway
The C4 pathway is used by plants such as...
45.6K
01:28Biosynthesis of Nucleic Acids
54
Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...
54
01:26Respiration Pathways
19
Cellular respiration is a fundamental metabolic process that enables organisms to generate energy from organic molecules. One of its central pathways is the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, which plays a crucial role in energy production and biosynthetic processes.Conversion of Pyruvate to Acetyl-CoAThe pyruvate generated from glycolysis undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex, producing acetyl-CoA, one molecule of NADH, and one...
19