不同的正统学推断算法在Brassicaceae物种中产生类似的预测正统组
Irene T Liao1, Karen E Sears1,2, Lena C Hileman3
1Department of Molecular, Cell, and Development Biology University of California - Los Angeles Los Angeles California USA.
Applications in plant sciences
|February 5, 2025
概括
像OrthoFinder,SonicParanoid和Broccoli这样的正统学推断算法对植物基因组是有效的. 结果与 ploidy 有所不同,这表明在比较基因组学中进行准确的 ortholog 识别的补充分析.
科学领域:
- 进行比较的基因组学.
- 生物信息学是一种生物信息学.
- 植物遗传学 植物遗传学
背景情况:
- 正理学推断对于比较基因组学至关重要,但由于复杂的基因组历史,对植物来说,工具选择具有挑战性.
- 现有基准可能无法完全捕捉植物基因组进化的细微差别.
研究的目的:
- 为了评估四个ortology推断算法 (OrthoFinder,SonicParanoid,Broccoli,OrthNet) 在Brassicaceae基因组上的性能.
- 评估算法在不同类型的化水平 (包括双化和多化) 上的适用性.
主要方法:
- 在八个Brassicaceae基因组上测试了OrthoFinder,SonicParanoid,Broccoli和OrthNet.
- 仅对双倍体数据集的算法性能进行比较,而不是包括中多多倍体和六倍体的数据集.
主要成果:
- 整形组的组成反映了物种多样性和进化历史.
- 只有双胞胎的集合显示了更多相同的正确组;然而,整体相似性在双胞胎水平上是可比的.
- 形寻找器,SonicParanoid和Broccoli提供了可靠的初始预测,而OrthNet提供了独特的对线性洞察力.
结论:
- 建议使用OrthoFinder,SonicParanoid和Broccoli来进行植物初始的ortology预测.
- OrthNet可以提供补充的对线性数据.
- 进一步的分析,如树推理,是必要的,以改进正统学预测,特别是复杂的植物基因组.
相关概念视频
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
02:05Gene Evolution - Fast or Slow?
7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.0K
03:21Phylogenetic Trees
45.1K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.1K
01:20Structural Classification of Joints
3.1K
Joints, also known as articulations, are classified based on their structural characteristics, i.e., based on whether the articulating surfaces of the adjacent bones are directly connected by fibrous connective tissue or cartilage, or whether the articulating surfaces contact each other within a fluid-filled joint cavity. These differences serve to divide the joints of the body into three structural classifications.
A fibrous joint is where the adjacent bones are united by fibrous connective...
A fibrous joint is where the adjacent bones are united by fibrous connective...
3.1K
02:47Protein Families
15.2K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.2K
02:27Predicting Molecular Geometry
34.0K
VSEPR Theory for Determination of Electron Pair Geometries
34.0K