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    Rice Genome

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    Pavani Gaja
    The document summarizes key details about the sequencing of the rice genome. It was the first crop plant genome to be fully sequenced. An international collaboration sequenced the rice genome between 1997-2004 using both map-based and shotgun sequencing methods. They produced a high-quality draft sequence covering over 90% of the rice genome. Significant findings included identifying over 37,000 protein-coding genes and revealing that transposable elements make up around 35% of the rice genome. The sequencing provided fundamental insights into rice biology, genetics and evolution.

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    Rice Genome

    Uploaded by

    Pavani Gaja
    632 views26 pages
    The document summarizes key details about the sequencing of the rice genome. It was the first crop plant genome to be fully sequenced. An international collaboration sequenced the rice genome between 1997-2004 using both map-based and shotgun sequencing methods. They produced a high-quality draft sequence covering over 90% of the rice genome. Significant findings included identifying over 37,000 protein-coding genes and revealing that transposable elements make up around 35% of the rice genome. The sequencing provided fundamental insights into rice biology, genetics and evolution.

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    The document summarizes key details about the sequencing of the rice genome. It was the first crop plant genome to be fully sequenced. An international collaboration sequenced the rice genome between 1997-2004 using both map-based and shotgun sequencing methods. They produced a high-quality draft sequence covering over 90% of the rice genome. Significant findings included identifying over 37,000 protein-coding genes and revealing that transposable elements make up around 35% of the rice genome. The sequencing provided fundamental insights into rice biology, genetics and evolution.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    632 views26 pages

    Rice Genome

    Uploaded by

    Pavani Gaja
    The document summarizes key details about the sequencing of the rice genome. It was the first crop plant genome to be fully sequenced. An international collaboration sequenced the rice genome between 1997-2004 using both map-based and shotgun sequencing methods. They produced a high-quality draft sequence covering over 90% of the rice genome. Significant findings included identifying over 37,000 protein-coding genes and revealing that transposable elements make up around 35% of the rice genome. The sequencing provided fundamental insights into rice biology, genetics and evolution.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
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    Sequencing of Rice genome

    Ch.Sreelakshmi
    TAD/13-17
    What is the rice genome?
     The world’s first genome of a crop plant that was
    completely sequenced
     Rice –like Arabidopsis –is a model
    experimental plant
    Model experimental crop: Why rice?

     Belongs to the grass family


     Has a much smaller genome and the greatest
    biodiversity of cereal crops
     Has a high degree of colinearity with the genomes
    of wheat, barley, and maize.
    Model experimental crop: Why rice?

     Rice has a simple genetic


    system (diploid and disomic
    inheritance)

     Has enormous number of


    genes controlling
    agronomically important traits;

     Wide genetic diversity is


    present in the genus Oryza.
    Milestones in the rice genome sequencing

    Sept 1997 – Sequencing of the


    rice genome was initiated
    as an international
    collaboration among 10
    countries

    Feb 1998 – IRGSP (International


    Rice Genome Sequencing Project)
    was launched under the
    coordination of the Rice Genome
    Program (RGP) of Japan
    Milestones in the rice genome sequencing
    April 2000 – Monsanto Co.
    produced a draft sequence of
    BAC contigs covering 260 Mb
    of the rice genome; 95%
    of rice genes were identified

    Feb 2001 – Syngenta produced a


    draft sequence and identified
    32,000 to 50,000 genes, w/ 99.8%
    sequence accuracy and identified
    99% of the rice genes
    An example of a genetic map of rice
    (chromosomes 1 and 2)
    Milestones in the rice genome sequencing
    Dec 2002 – IRGSP finished high-
    quality draft sequence (clone- by-
    clone approach) with a sequence
    length, excluding overlaps, of 366
    Mb
    corresponding to ~92% of the
    rice genome.
    Dec 2004 – IRGSP produce the
    high-quality’ sequence of the
    entire rice genome; with
    99.99% accuracy and without
    any sequence gap
    Chromosome assignment of the
    participating countries in the IGRSP
    How rice was sequenced?
    Map-based sequencing - each stretch of sequence is
    physically anchored to a chromosome forming a contig
    of clones, which are individually sequenced
    How rice was sequenced?
     Shotgun sequencing involves generation of short DNA fragments that are then
    sequenced & linearly arranged

     It enables full coverage of the genome in a fraction of the time required for the
    alternative BAC sequencing approach

     Physical mapping and sequencing: 9 genomic libraries used by PCR screening


    fingerprinting and end sequencing

     Sequences are assembled by using PHRED and PHRAP soft ware packages or
    TIGR assembler.

     Annotation and bioinformatics: gene models were predicted using FGENESH

     Interproscan: conserved domain search and and association with gene ontologies.

     BLASTP: for searching the predicted rice proteome.

     BLASTN: to find the location of snoRNAs and spliceosomal RNAs in the


    pseudomolecules.
    Who are the key players in sequencing projects?

    Research Institution Sequencing method


    International Rice Genome Map-based sequencing
    Sequencing Project (IRGSP)
    Beijing Genomics Institute (BGI) Shot-gun sequencing
    Monsanto Co. (funded
    University of Washington – Map-based sequencing
    Leroy Hood’s et al.)
    Syngenta-Myriad (funded Torrey
    Mesa Research Institute) Shot-gun sequencing
    Significant findings from the sequencing of rice genome
     Sequenced segment represents 99% of euchromatin and 95% of rice genome

     Non-Transposable element related protein coding sequences: 37544


     Gene density: 9.9 kb/gene
     2859 genes unique to rice and other cereals 11847 Tos 17 retrotransposable
    insertion sites, of which 3243 are in genes
     Transposan content of rice: 35% chromosome 8 and 12 have the highest
    (38% & 38.3%) and chromosome 1 (31.0%), 2 (29.8%) and 3 (29.0%) has the
    lowest transposan content.
     SNP frequency varies from 0.53-0.78%
     Mitochandrial genome: 600Kb, Chloroplast genome: 150 kb
     763 tRNAs including 14 tRNA pseudogenes 12 pseudomolecules.
     158 miRNAs, 215 small nucleolar RNAs, 93 spliceosomal RNA genes
    Features Draft sequence
    Nipponborne
    Gene size 2.4
    Gene density(kb/gene) 5.7
    No.of exons/gene 4.2
    Exon size (bp) 296
    No.of introns/gene 3.2
    Intron size (bp) 371
    CG content in coding region(%) 54.9
    CG content in coding region(%) 38.9
    CG content overall (%) 44.0
    Physical distance /genetic distance 253 kb/cM
    Genome size (Mb) 420
    Copy no (x103) Cove249.3rage (kb) Fraction of genome (%)

    Class 1 (Concentrated in gene poor , heterochromatic regions like centromeric and pericentromeric regions)

    LINEs 9.6 4161.3 1.12

    SINEs 1.8 209.9 0.06

    Ty1/copia 11.6 14266.7 3.85

    Ty3/gypsy 23.5 40363.3 10.90

    Other class 1 15.4 12733.3 3.43

    Total class 1 61.9 71734.4 19.35

    Class II (Terminal inverted repeats)

    hAT 1.1 1405.9 0.38

    CACTA 10.8 9987.3 2.69

    IS630/Tc1/mariner 67.0 8388.3 2.26

    IS 256/Mutator 8.8 13485.7 3.64

    IS 5/ Tourist 57.9 12095.8 3.26

    Other class II 18.2 2703.6 0.73

    Total class II 163.8 48066.6 12.96

    Other TEs 23.6 6797.7 1.80

    Total TEs 249.3 129019.3 34.79


    The rice genome holds fundamental
    information in its biological "power",
    including physiology, development,
    genetics, and molecular evolution.
    Thank you

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