洛根:行星规模的基因组组合调查了生命的多样性
Rayan Chikhi1, Téo Lemane2, Raphaël Loll-Krippleber3,4
1Institut Pasteur, Université Paris Cité, CNRS UMR3525, Paris, France.
bioRxiv : the preprint server for biology
|September 15, 2025
概括
洛根是一个新的大规模序列组件,它将公共序列数据转换为可搜索的连接. 这使得能够快速发现新型酶,扩大已知的遗传多样性,并促进全球健康和生态研究.
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.
- 分子生物学分子生物学
背景情况:
- 公开的核酸测序数据,特别是来自测序读取档案 (SRA) 的核酸测序数据,提供了对遗传多样性的洞察力,但由于数据的快速增长,面临分析挑战.
- 该SRA包含2730万个数据集 (5×10^16个基数对),代表了生物发现的庞大但未得到充分利用的资源.
研究的目的:
- 开发一个可扩展的解决方案来分析大量的序列读取档案 (SRA) 数据.
- 为了实现高效的,行星规模的序列搜索和发现新的生物实体和功能.
主要方法:
- 洛根的构建,一个巨大的序列组件,将短读数转换为长连接,并实现超过100倍的数据压缩.
- 开发了Logan-Search,这是Logan的k-mer索引,用于快速的,petabase规模的序列相似性搜索.
主要成果:
- 识别了超过2亿种塑料降解酶同类物,包括具有优越催化活性的新型酶.
- 蛋白质 (30倍),等离子体 (22倍),P4卫星 (4.5倍) 和Obelisk RNA元素 (3.7倍) 的已知多样性显著扩大.
- 实现了对抗微生物耐药性基因的全球跟踪,并对数百万个人类生物样本的病毒活性化进行了表征.
结论:
- 洛根改变了SRA,民主化了对大规模分析的公共遗传数据的访问.
- 洛根框架在生物技术,分子生态学和全球卫生研究方面开辟了新的前沿,通过有效的数据挖掘.
更多相关视频
08:36The Immersive Cleveland Clinic Virtual Reality Shopping Platform for the Assessment of Instrumental Activities of Daily Living
Published on: July 28, 2022
4.3K
04:20Author Spotlight: Exploring Microglial Interactions with Stress-Response Circuitry Using the Limited Bedding and Nesting Model
Published on: July 12, 2024
2.4K
相关概念视频
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
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...
02:54Evolutionary Relationships through Genome Comparisons
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...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
03:21Genome Size and the Evolution of New Genes
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.
01:08Evolution of Microbial Genome
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.