星际飞船巨型可转移元素按宿主分类学集群使用基于k-mer的基因组学
Rowena Hill1, Daniel Smith2, Gail Canning3
1Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK.
G3 (Bethesda, Md.)
|April 11, 2025
概括
星际飞船,巨大的真菌可转移元素,使用k-mer遗传学进行了新分类. 这种方法揭示了基于宿主分类学和货物基因的元素关系,而不仅仅是船长基因.
科学领域:
- 菌类学和基因组学 菌类学和基因组学
- 可转移的元素可以转移.
- 人类遗传学 是一个学科.
背景情况:
- 星际飞船是真菌 (Pezizomycotina) 中的大型可转移元素,高达700kbp,携带众多辅助基因.
- 目前的分类依赖于氨酸复合酶基因 (captain),这可能不完全代表元素相关性.
- 星际飞船长度和货物含量的高变化给全面分析带来了挑战.
研究的目的:
- 开发和应用一种基于k-mer的新型遗传学方法来分析星际飞船元素的相关性.
- 为了比较从整个元素推断出的星际关系与仅从船长基因推断出的星际关系.
- 研究宿主分类学和货物基因含量对星际飞船进化和转移的影响.
主要方法:
- 利用无对齐的基于k-mer的遗传树构建方法来分析整个星际飞船元素.
- 与基于船长基因的基因相比,k-mer衍生的星际飞船系.
- 检查了Gaeumannomyces物种的星际飞船,以与货物基因相似性相关联的基因关系.
主要成果:
- 基于K-mer的族系学揭示了与仅仅从船长基因推断出的星际关系不同.
- 使用k-mers确定的元素相关性模式与真菌宿主分类学相对应.
- 在Gaeumannomyces中,k-mer关系与货物基因内容的相似性保持一致,表明其重要性.
结论:
- 基于K-mer的家族遗传学提供了一种强大的方法来全面分析高度可变的星际飞船元素.
- 这种方法凸显了货物基因和宿主基因在塑造星际飞船进化的重要性.
- 这些发现提供了关于菌中星际船介导的水平基因转移事件的动态的见解.
相关概念视频
02:54Evolutionary Relationships through Genome Comparisons
5.6K
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...
5.6K
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
02:13Overview of Transposition and Recombination
15.1K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
15.1K
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
11.9K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
11.9K
03:21Phylogenetic Trees
44.9K
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.
44.9K
01:23Phylogeny
43.4K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
43.4K