科尔吉亚斯:通过考虑大型 prokaryotic 基因组数据集中的进化历史来识别相关的基因对
Yuki Nishimura1, Kimiho Omae1,2, Kento Tominaga1,3
1Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-0882, Japan.
NAR genomics and bioinformatics
|December 15, 2025
概括
开发了两种新的遗传学方法,即祖先状态调整 (ASA) 和同时进化试验 (SEV),用于在 prokaryotic 基因组中注释 ortholog 组 (OG). 这些方法改善了对未表征的基因的功能推断,特别是在大型元基因组数据集中.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 进化生物学 进化生物学
背景情况:
- Prokaryotic 基因组扩张产生了许多不具特征的 Ortholog 组 (OG).
- 基于序列相似性的注释与这些OG斗争,特别是在元基因组组装基因组中.
- 遗传学分析提供了一个有前途的替代方案,通过分析OG分布模式.
研究的目的:
- 为大规模基因组数据分析引入两种新型遗传学方法,即祖先状态调整 (ASA) 和同时进化试验 (SEV).
- 评估ASA和SEV的性能与现有的注释ortolog组方法相比.
- 探索 ASA 和 SEV. 所识别的功能关系类型.
主要方法:
- 祖先状态调整 (ASA) 和同时进化测试 (SEV) 方法的开发.
- 在家族遗传学分析中考虑祖先状态的ortolog组存在/缺席.
- 使用比较性能分析对三种不同的 prokaryotic 数据集的评估.
- 用矩阵乘法来评估可扩展性的应用.
主要成果:
- 在大规模的 prokaryotic 数据集上,ASA 和 SEV 显示出与既定和最新方法相比具有可比或优越的性能.
- SEV及其前身有效地识别了缓慢演变的正统组,包括家政基因.
- ASA及其前身确定了功能相关的正统组,具有保留的收益/损失模式,这表明了进化约束.
结论:
- ASA和SEV是有效的家族遗传学方法,用于推断 prokaryotic 基因组中未表征的正统组的功能推断.
- 这些方法提供了基于进化模式的基因功能的互补见解.
- 对于广泛的基因组数据库的分析,SEV是可扩展的.
相关概念视频
Evolutionary Relationships through Genome Comparisons
6.8K
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...
6.8K
Gene Evolution - Fast or Slow?
7.9K
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...
7.9K
Gene Evolution - Fast or Slow?
3.4K
3.4K
Genome Size and the Evolution of New Genes
8.9K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.9K
Genome Size and the Evolution of New Genes
3.2K
3.2K
Genomic DNA in Prokaryotes
48.2K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic Diversity in Bacteria
Although bacterial genomes are much...
48.2K


