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Related Concept Videos

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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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.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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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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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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Comparative genomics reveals intraspecific divergence of

Rui Liu1, Liyuan Ma1,2,3, Hongmei Wang1,2,4

  • 1Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China.

Microbial Genomics
|June 7, 2023
PubMed
Summary

Acidithiobacillus ferrooxidans, a model organism for extreme environments, shows significant intra-species divergence. Comparative genomics reveals evolutionary trends and key genetic differences contributing to adaptation.

Keywords:
Acidithiobacillus ferrooxidanscomparative genomicsenvironmental adaptationevolutionary processintraspecific divergence

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Area of Science:

  • Microbial Evolution
  • Extremophile Biology
  • Genomics

Background:

  • Acidithiobacillus ferrooxidans is a model chemolithoautotroph thriving in extreme acid conditions, known for unique metabolism and adaptability.
  • Limited understanding exists regarding the evolutionary divergences within A. ferrooxidans based on whole-genome analysis.

Purpose of the Study:

  • To investigate intra-species evolutionary divergences in Acidithiobacillus ferrooxidans using comparative genomics.
  • To explore genome size trends, gene gain/loss dynamics, and identify genes under positive selection.
  • To correlate genetic differences, such as rusticyanin sequences and type IV secretion systems, with observed group divergences.

Main Methods:

  • Isolation of six A. ferrooxidans strains from mining areas in China and Zambia.
  • Comparative genomics analysis of isolated strains.
  • Ancestral genome reconstruction to infer evolutionary trends.
  • Identification of genes under positive selection and analysis of key protein sequences (e.g., rusticyanin) and systems (e.g., T4SS).

Main Results:

  • A. ferrooxidans diverged into three distinct groups from a common ancestor, with an 'open' pan-genome.
  • Genome size initially increased then decreased during evolution, indicating significant gene gain and loss.
  • Twenty-three single-copy orthologous groups were identified as being under positive selection.
  • Differences in rusticyanin sequences and type IV secretion system composition correlate with group divergence and intraspecific diversity.

Conclusions:

  • Comparative genomics provides insights into the divergent evolution and adaptation of A. ferrooxidans at the genome level.
  • Gene gain and loss dynamics are critical for genome flexibility and adaptation in extreme environments.
  • Specific genetic elements like Rus and T4SS contribute significantly to the intraspecific diversity of A. ferrooxidans.