全基因组适应的架构在实验进化的Drosophila中,其特点是广泛的类型
Zachary S Greenspan1, Thomas T Barter, Mark A Phillips
1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA. ldmuelle@uci.edu.
Journal of genetics
|January 23, 2024
概括
了解适应需要整合基因组和转录组数据. 机器学习揭示了SNP和可转移元素等遗传变异显著影响基因表达,在不断发展的种群中塑造复杂的特征.
科学领域:
- 进化生物学是进化的生物学.
- 基因组学就是基因组学.
- 系统生物学 系统生物学
背景情况:
- 适应的分子基础是不太了解的.
- 基因组研究往往侧重于选择的异构性签名.
- 进化中的基因表达变化通常与遗传原因无关.
研究的目的:
- 在适应过程中探索基因组,转录组和表型之间的相互作用.
- 利用机器学习来剖析适应机制.
- 为了研究Drosophila生命史进化的遗传基础.
主要方法:
- 在相反的选择压力下,Drosophila种群经过实验进化.
- 应用机器学习工具来分析基因组和转录基因组数据.
- 基因变异 (SNP,TE,indels) 与基因表达模式的相关性.
主要成果:
- 基因组和转录组数据显示出相似的表型预测能力.
- 众多的基因组部位会影响个体的转录表达.
- SNPs,可转移元素和indels是基因表达的强有力的预测因素.
结论:
- 适应的基因组架构是高度多基因的.
- 广泛的类型是适应性进化的基础.
- 机器学习有效地整合了多omics数据,以揭示适应机制.
相关概念视频
Position-effect Variegation
6.3K
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
6.3K
Exon Recombination
3.6K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...
Exon shuffling follows “splice frame rules.” Each exon...
3.6K
Background and Environment Affect Phenotype
6.5K
Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
6.5K
Genetic Screens
4.9K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
4.9K
Limits to Natural Selection
31.3K
Organisms that are well-adapted to their environment are more likely to survive and reproduce. However, natural selection does not lead to perfectly adapted organisms. Several factors constrain natural selection.
31.3K


