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Related Experiment Videos

Highly asymmetric rice genomes.

Jing Ding1, Hitoshi Araki, Qiang Wang

  • 1State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China. dingjing@nju.org.cn <dingjing@nju.org.cn>

BMC Genomics
|June 9, 2007
PubMed
Summary

Genomic analysis of two rice varieties reveals significant gene repertoire polymorphism, with at least 10% of genes showing presence/absence or asymmetric locations. This genomic asymmetry, particularly in disease resistance genes, suggests natural selection plays a role in rice genome evolution.

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Area of Science:

  • Genomics
  • Plant Genetics
  • Evolutionary Biology

Background:

  • Genomic sequencing assumes shared gene sets within a species, but structural rearrangements are common.
  • Polymorphism in gene content and location can occur even within the same species.
  • Two rice genomes (Oryza sativa L. var. Nipponbare and O. sativa L. var. 93-11) offer a model for studying gene repertoire variation.

Purpose of the Study:

  • To systematically investigate gene repertoire polymorphism between two rice genomes.
  • To compare gene content and genomic locations to identify asymmetric genes.
  • To explore the role of natural selection in maintaining genomic asymmetry.

Main Methods:

  • Comparative genomics of two rice varieties (Nipponbare and 93-11).
  • Analysis of gene presence/absence and genomic locations.

Related Experiment Videos

  • Proportion calculation of asymmetric genes across different gene groups.
  • Nucleotide diversity analysis of selected genes.

    • Main Results:

    • At least 10% of genes exhibit presence/absence polymorphism (5.2%) or asymmetric locations (4.7%) between the two rice genomes.
    • Disease resistance (R) genes and RLK kinase genes show a disproportionately higher percentage of asymmetric genes compared to housekeeping genes.
    • Low nucleotide diversity (0.0051) was observed in 17 R genes under presence/absence polymorphism.
    • Natural selection is implicated in maintaining genomic asymmetry.

    Conclusions:

    • Genomic symmetry is disrupted by approximately 10% of asymmetric genes, potentially increasing genetic variation.
    • Asymmetric genes may lead to unequal crossing over during meiosis in heterozygotes.
    • Diversifying selection may drive structural divergence, while purifying selection maintains low nucleotide divergence within R gene loci.