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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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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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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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Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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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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Phylogenetic Trees03:21

Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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Related Experiment Video

Updated: Jun 6, 2025

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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What Are We Learning from Plant Pangenomes?

Murukarthick Jayakodi1,2, Hyeonah Shim3, Martin Mascher4,3

  • 1Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA;

Annual Review of Plant Biology
|December 2, 2024
PubMed
Summary

A pangenome, integrating multiple genomes, captures species diversity better than a single reference. Advanced sequencing and graph-based systems are improving plant pangenomics, but challenges remain in data analysis and interpretation.

Keywords:
DNA sequencinggraph-based pangenomepangenomespecies diversitystructural variation

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Last Updated: Jun 6, 2025

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • A single reference genome is insufficient for capturing the full genetic diversity within a species.
  • Pangenomes integrate multiple genomes to represent the complete set of nonredundant genes and genome diversity.
  • Advancements in sequencing technologies allow for precise cataloging of genetic variations.

Purpose of the Study:

  • To highlight the importance and evolution of pangenomics in plant research.
  • To discuss the applications of pangenomic studies in understanding plant traits and evolution.
  • To identify current challenges and future needs in the field of plant pangenomics.

Main Methods:

  • Incorporating multiple genomes to construct a comprehensive species-wide gene set.
  • Utilizing advanced sequencing technologies for high-quality genome assembly and variation detection.
  • Developing graph-based reference systems for representing complex genomic structures.

Main Results:

  • Pangenomic studies have successfully identified structural variants in plant genomes.
  • The genetic architecture of agronomic traits has been dissected using pangenomic approaches.
  • Pangenomes aid in unraveling the molecular basis and evolutionary history of plant phenotypes.

Conclusions:

  • The pangenome concept has evolved to super-pangenomes, including wild relatives and employing graph-based references.
  • Significant challenges persist in building pangenomes and representing structural variants, particularly in crops.
  • Standardized computational pipelines, common data structures, new algorithms, and increased data storage are crucial for advancing plant pangenomics.