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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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The 3,000 rice genomes project.

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    |May 30, 2014
    PubMed
    Summary

    Researchers resequenced 3,000 rice genomes, discovering 18.9 million single nucleotide polymorphisms (SNPs). This genomic data enhances understanding of rice diversity and aids in developing improved rice varieties for global food security.

    Area of Science:

    • Genomics
    • Plant Science
    • Agricultural Science

    Background:

    • Rice (Oryza sativa L.) is a global staple food, crucial for feeding over half the world's population.
    • Projected population growth necessitates a 25% increase in rice production by 2030.
    • Climate change and land scarcity demand accelerated genetic improvements in rice.

    Purpose of the Study:

    • To conduct an international resequencing of 3,000 diverse rice accessions.
    • To generate a comprehensive genomic dataset for rice.
    • To facilitate the discovery of novel alleles for improved rice phenotypes.

    Main Methods:

    • Resequencing of 3,000 rice genomes from 89 countries.
    • Bioinformatic analysis of sequencing data against the Nipponbare reference genome.
    Keywords:
    Genetic resourcesGenome diversityNext generation sequencingOryza sativaSequence variants

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  • Phylogenetic analysis using single nucleotide polymorphism (SNP) data.

    • Main Results:

    • Sequencing achieved an average depth of 14× with 94.0% genome coverage.
    • Approximately 18.9 million single nucleotide polymorphisms (SNPs) were identified.
    • Phylogenetic analysis revealed 5 distinct varietal groups within Oryza sativa.

    Conclusions:

    • An international effort has resequenced 3,000 rice genomes, providing a foundational dataset.
    • The data enables large-scale discovery of novel alleles for important rice traits.
    • The study advocates for a global, public rice genetic database to advance breeding technology.