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Related Concept Videos

Genomics02:02

Genomics

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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...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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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...
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Taxonomy01:31

Taxonomy

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Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics. It uses a hierarchy of increasingly inclusive categories with Latin names. The smallest units of taxonomy, species and genus, are used to assign a formal, taxonomic name to each species in a system. This classification system, referred to as binomial nomenclature, was formalized by Carolus Linnaeus in the 18th century.
Hierarchy of Taxonomy
The hierarchy that Carolus Linnaeus first...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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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.
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A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy.

Ming-Hsin Tsai1, Yen-Yi Liu2, Von-Wun Soo3

  • 1Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 35053, Taiwan. skypea@nhri.org.tw.

Microorganisms
|June 6, 2019
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Summary

Microbial classification faces challenges with new sequencing data. A genome-wide comparison using homologous coverage ratio (HCR) offers a more reliable method than marker genes for accurate microbial taxonomy.

Keywords:
bacterial classificationbacterial identificationmicrobial taxonomywhole genome comparison

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing has increased the number of sequenced microbial genomes, including previously unculturable bacteria.
  • This expansion complicates microbial classification and highlights challenges in assigning accurate taxonomic names.
  • Assessing the consistency between genomic relatedness and current taxonomy is crucial for microbial diversity studies.

Purpose of the Study:

  • To propose and apply a genome comparison approach for investigating genomic differences among microorganisms.
  • To evaluate the effectiveness of the homologous coverage ratio (HCR) criterion for microbial classification.
  • To compare the performance of HCR with average nucleotide identity (ANI) and marker gene-based approaches.

Main Methods:

  • A large-scale survey of 7861 microbial genomes (excluding plasmids) was conducted.
  • The homologous coverage ratio (HCR), a genome-wide criterion, was used to describe homology between species.
  • HCR and average nucleotide identity (ANI) were compared, and the Genome Taxonomy Database (GTDB) was used for validation.

Main Results:

  • The analysis identified 1220 pairs of genera with ambiguous classifications.
  • HCR and ANI analyses produced comparable results, with HCR showing a potentially superior clustering effect in some cases.
  • Validation with the GTDB indicated limitations in marker gene-based classification, including boundary blur between genera and unavoidable marker gene selection bias.

Conclusions:

  • Genome-wide comparison methods, such as HCR, should be considered for microbial classification to overcome the limitations of marker gene-based approaches.
  • The current microbial classification system requires re-examination using genome-wide comparisons to better reflect microbial diversity.
  • Addressing taxonomic challenges is essential for advancing our understanding of microbial communities and their roles.