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Meloidogyne comparative genomics

Dave Lunt
September 01, 2016

Meloidogyne comparative genomics

The origins, species structure, diversity, and ploidy of globally important crop pests

Dave Lunt

September 01, 2016
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  1. MELOIDOGYNE COMPARATIVE
    GENOMICS
    ORIGINS, SPECIES STRUCTURE, DIVERSITY
    AND PLOIDY OF GLOBALLY IMPORTANT
    CROP PESTS
    AMIR SZITENBERG, LAURA SALAZAR, VIVIAN BLOK,
    SOUMI JOSEPH, DOMINIK LAETSCH, VALERIE
    WILLIAMSON, MARK BLAXTER, DAVE LUNT
    @davelunt
    [email protected] speakerdeck.com/davelunt
    slides:

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  2. MELOIDOGYNE COMPARATIVE
    GENOMICS
    THANKS:
    NERC, AFRICA GOMEZ, CHARLES OPPERMAN, DAVID BIRD,
    ETIENNE DANCHIN, PHILIPPE CASTAGNONE-SERENO, BOB
    ROBBINS, PABLO CASTILLO & MANY MANY OTHERS
    @davelunt
    [email protected]
    speakerdeck.com/davelunt
    slides available
    data accession: PRJNA340324
    Amir Szitenberg & Laura Salazar have carried out most of this work

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  4. 18S structural alignment ML tree

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  5. M. incognita Abad et al 2008
    M. hapla Opperman et al 2008
    M. floridensis Lunt et al 2011
    M. chitwoodi SRA ERX1284800 Bird et al

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  6. MIG: THE MELOIDOGYNE INCOGNITA GROUP GENOMES
    MIG GENOME SEQUENCES PRESENTED TODAY
    8 M. incognita
    5 M. javanica
    3 M. arenaria
    2 M. floridensis
    Primary high quality dataset
    1 M. enterolobii
    outgroup
    Each provides compete
    mitochondrial and nuclear
    genomes
    MIG

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  7. MITOCHONDRIAL GENOME PHYLOGENY
    MIG species are
    resolved by mtDNA
    Close relatives; they
    show very little
    divergence
    Concatenated genes, ML tree, RAxML
    MIG

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  8. NUCLEAR GENOMES
    GENOMES ARE COMPLEX, CONTAINING TWO
    DIVERGENT GENOME COPIES
    ORTHOLOGOUS LOCI MUST BE CORRECTLY
    IDENTIFIED

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  9. INTRASPECIFIC BLAST SHOWS 2 DIVERGENT GENOME COPIES
    divergence of
    copy A and copy B
    M. hapla and M. chitwoodi
    do not have divergent genomic copies

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  10. THE MELOIDOGYNE INCOGNITA GROUP GENOMES
    2 DIVERGENT GENOME COPIES IN ALL MIG
    A
    B
    Single origin of 2 genome
    copies predating speciation
    Phylogeny within each
    genome copy A/B is
    identical
    M. incognita M. javanica M. arenaria M. floridensis
    Orthologue CDS supermatrix ML tree RAxML

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  11. annotated
    unannotated
    genes mostly
    Intergenic DNA
    Stacked bar charts representing estimated genome
    size and content
    Repetitive elements
    SSRs
    Transposons
    homozygous
    B
    A1
    A2
    B
    A1
    A2
    B
    A1
    A2
    B
    A
    GENOME SIZE

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  12. THE MELOIDOGYNE INCOGNITA GROUP GENOMES
    TROPICAL APOMICTS ARE HYPOTRIPLOIDS
    copy A1 copy B
    copy A2
    copy number
    1
    2
    A1-A2 are ~100% identical to each other
    copy A copy B
    copy number
    1
    2
    3% divergence in protein coding regions
    illustration of diversity at each
    diploid locus
    Some loci are diploid A,B, some triploid A1,A2,B
    illustration of diversity at each
    triploid locus
    hypotriploid = not full triploid, some parts of genome are diploid

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  13. THE MELOIDOGYNE INCOGNITA GROUP GENOMES
    TROPICAL APOMICTS ARE HYPOTRIPLOIDS
    illustration of diversity at each triploid locus
    not all loci are triploid, diploid loci add to
    read depth 100 peak
    many loci have
    read depth 100
    some loci have
    read depth 200
    A1 + A2
    from M. javanica high quality PacBio genome
    copy A1 copy B
    copy A2
    copy number
    1
    2
    sequence read depth
    A + B

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  14. POPULATION GENOMICS
    INTRASPECIFIC WORLDWIDE GENOMIC DIVERSITY IS V LOW
    1% gene sequence divergence
    isolate source location
    A14 Vivian Blok Libya
    L27 Vivian Blok USA race 1
    VW6 Valerie Williamson USA, California
    W1 Valerie Williamson USA
    HarC Valerie Williamson USA
    L19 Vivian Blok West Indies
    L9 Vivian Blok Africa, Ivory Coast
    Meloidogyne incognita genomes
    Orthologue CDS supermatrix ML tree RAxML

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  15. SUMMARY
    A1
    A2
    B
    Techniques not accounting for divergent genomes will
    have problems representing species relationships &
    diversity
    MIG have 2 divergent genomic copies
    Divergence preceded speciation with
    likely hybrid origin
    Some genomic regions are triploid

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  16. A COMMUNITY OF MELOIDOGYNE GENOMICS
    OPEN DATA SHARING
    LETS TALK
    Better science will be done, and more
    problems will be solved, with data
    freely and immediately available to all
    We need to
    collaborate, build
    community, & use
    Large scale functional genomics is a reality
    @davelunt
    [email protected]
    speakerdeck.com/davelunt
    slides available
    metadata; know your enemy
    data accession: PRJNA340324
    both raw data and genome assemblies

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