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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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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.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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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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Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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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.
In contrast, regions which code...
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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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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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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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Related Experiment Video

Updated: Jul 2, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution.

Víctor Roces1, Sara Guerrero1, Ana Álvarez1

  • 1Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Asturias, Spain.

Molecular Biology and Evolution
|February 27, 2024
PubMed
Summary

PlantFUNCO database integrates diverse plant genomics data to reveal functional conservation across species. This resource aids in understanding epigenome evolution and genetic redundancy, validated by mutant phenotypes.

Keywords:
databaseevolutionary epigenomicsfunctional genomicsintegrative approachparalogs

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
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Last Updated: Jul 2, 2025

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

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Area of Science:

  • Evolutionary epigenomics
  • Evolutionary functional genomics
  • Plant comparative genomics

Background:

  • Non-DNA-encoded alterations in gene expression are crucial for plant plasticity and adaptation.
  • Previous plant comparative genomics studies primarily used same-assay data, limiting conservation inference.
  • Heterogeneous datasets offer powerful insights into evolutionary conservation.

Purpose of the Study:

  • To introduce the PlantFUN(ctional)CO(nservation) database (PlantFUNCO) for inferring functional genomics conservation.
  • To analyze interspecies chromatin states and functional genomics conservation scores in key plant models.
  • To provide a novel resource for comparative genomics and evolutionary studies in plants.

Main Methods:

  • Development of the PlantFUNCO database integrating diverse functional genomics datasets.
  • Analysis of chromatin states and conservation scores across Arabidopsis thaliana, Oryza sativa, and Zea mays.
  • Replication of genetic redundancy models and validation using mutant phenotypes under stress.

Main Results:

  • PlantFUNCO successfully elucidated evolutionary information through cross-species functional agreement.
  • Chromatin states were identified as key determinants of paralog functional divergence in Arabidopsis thaliana.
  • Predictions of genetic redundancy were validated by experimental data from mitochondrial alternative oxidase mutants.

Conclusions:

  • PlantFUNCO offers a complementary resource for comparative genomics, leveraging data diversity to study plant epigenome evolution.
  • The database facilitates extrapolation of molecular mechanisms across model organisms to assess functional conservation.
  • Understanding functional conservation deepens insights into plant epigenome and noncoding genome evolution.