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Related Concept Videos

Genomics02:02

Genomics

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...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing 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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary 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...
Genome Annotation and Assembly03:36

Genome 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.
Genome Size and the Evolution of New Genes03:21

Genome 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.
Evolution of Microbial Genome01:08

Evolution 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.

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Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.

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
PubMed
Summary
This summary is machine-generated.

Logan is a new massive sequence assembly that transforms public sequencing data into searchable contigs. This enables rapid discovery of novel enzymes, expands known genetic diversity, and facilitates global health and ecological research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Public nucleic acid sequencing data, particularly from the Sequence Read Archive (SRA), offers insights into genetic diversity but faces analysis challenges due to rapid data growth.
  • The SRA contains 27.3 million datasets (5 × 10^16 basepairs), representing a vast but underutilized resource for biological discovery.

Purpose of the Study:

  • To develop a scalable solution for analyzing the massive Sequence Read Archive (SRA) data.
  • To enable efficient, planetary-scale sequence searching and discovery of novel biological entities and functions.

Main Methods:

  • Construction of Logan, a massive sequence assembly transforming short reads into long contigs and achieving over 100-fold data compression.
  • Development of Logan-Search, a k-mer index of Logan for rapid, petabase-scale sequence similarity searches.

Main Results:

  • Identification of over 200 million plastic-degrading enzyme homologs, including novel enzymes with superior catalytic activity.
  • Significant expansion of known diversity for proteins (30-fold), plasmids (22-fold), P4 satellites (4.5-fold), and Obelisk RNA elements (3.7-fold).
  • Enabled global tracking of antimicrobial resistance genes and characterization of viral reactivation across millions of human BioSamples.

Conclusions:

  • Logan transforms the SRA, democratizing access to public genetic data for large-scale analysis.
  • The Logan framework opens new frontiers in biotechnology, molecular ecology, and global health research by enabling efficient data mining.