微生物基因组的压缩率与基因组大小和基组成有关
Jon Bohlin1, John H-O Pettersson2,3,4
1Norwegian Institute of Public Health, Domain for Infection Control, Section for Modeling and Bioinformatics, Oslo, Norway. jon.bohlin@fhi.no.
Genomics & informatics
|October 10, 2024
概括
微生物基因组的压缩性,与大小和AT含量相关,影响突变积累. 寡核酸使用变异 (OUV) 有效预测基因组可压缩性.
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.
- 计算生物学 计算生物学
背景情况:
- 字符串的压缩性与复杂性和信息潜力相关.
- 微生物基因组在大小和基成分 (AT/GC含量) 中表现出显著的变化.
- 基因组合影响DNA单词频率,从而影响基因组的可压缩性.
研究的目的:
- 为了研究微生物基因组的压缩性.
- 检查压缩性,基因组大小,AT含量和寡核酸使用变异 (OUV) 之间的关联.
- 为了比较基于DNA (MBGC) 和通用 (ZPAQ) 压缩算法的性能.
主要方法:
- 分析了4713个RefSeq微生物基因组.
- 应用通用添加模型来评估关联.
- 使用了MBGC和ZPAQ压缩算法.
- 评估基因组大小,AT含量和OUV作为影响压缩性的因素.
主要成果:
- 基因组大小和OUV与两种压缩机的基因组冗余密切相关.
- 平均而言,MBGC比ZPAQ提供了3%的压缩改进.
- 与ZPAQ不同的是,MBGC在AT贫乏和AT丰富基因组之间发现了显著的压缩比差异.
结论:
- 较小,富含AT的基因组可能因压缩能力较低而存在更多的随机突变.
- 较大,AT-贫乏的基因组更多余.
- 超紫外线是微生物基因组压缩性的强有力的预测指标.
- 一般来说,ZPAQ与MBGC一致,但效果不那么好,特别是在AT丰富/贫困基因组方面.
相关概念视频
Genomic DNA in Prokaryotes
43.5K
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...
43.5K
Genome Size and the Evolution of New Genes
7.9K
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.
7.9K
The Nucleosome
1.4K
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
1.4K
Gene 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
Genomic DNA in Eukaryotes
46.7K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
46.7K
Chromatin Packaging
16.6K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
16.6K


