Upgrade to Pro — share decks privately, control downloads, hide ads and more …

Root Knot Nematodes: understanding their evolution, diversity, and threat through comparative genomics

Dave Lunt
December 16, 2014

Root Knot Nematodes: understanding their evolution, diversity, and threat through comparative genomics

Talk to Association of Applied Biologists

Dave Lunt

December 16, 2014
Tweet

More Decks by Dave Lunt

Other Decks in Science

Transcript

  1. Root Knot Nematode Genomes
    JD Eisenback
    RKN
    juveniles
    enter root tip
    SEM Meloidogyne female
    JD Eisenback
    Understanding their evolution,
    diversity and threat through
    comparative genomics
    Amir Szitenberg
    Georgios Koutsovoulos
    Mark Blaxter
    Sujai Kumar
    Evolutionary Biology Group, University of Hull
    Institute of Evolutionary Biology, University of Edinburgh
    @davelunt
    speakerdeck.com/davelunt
    slides available
    Dave Lunt

    View Slide

  2. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Root Knot Nematodes
    • Globally important agricultural pest species
    • ~5% loss of world agriculture
    • Enormous plant host range
    • parasitise all main crop plants
    JD Eisenback
    RKN
    juveniles
    enter root tip
    infected uninfected
    SEM Meloidogyne female
    JD Eisenback

    View Slide

  3. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Reproduction
    • Mitotic parthenogens (apomixis) without
    chromosome pairs.
    Asexuals- meiosis absent
    • Meiotic parthenogens (automixis)
    • Obligatory outbreeding sexuals with
    males & females (amphimixis)
    Sexuals- meiosis present
    Wide variety of reproductive modes in a single genus

    View Slide

  4. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Reproduction
    Wide variety of reproductive modes in a single genus

    View Slide

  5. MELOIDOGYNE HYBRIDISATION
    Hybrid Speciation
    Once thought that
    hybrid speciation was
    rare and inconsequential
    in animals
    Genome biology is
    revealing a very different
    view
    Heliconius butterflies
    Lak Malawi cichlids
    Polar and brown bears

    View Slide

  6. MELOIDOGYNE HYBRIDISATION
    Hybrid Speciation in Meloidogyne?
    Previous work suggests
    interspecific
    hybridisation may be
    involved with
    Meloidogyne asexual
    species
    Heliconius butterflies
    Lake Malawi cichlids
    Root knot nematodes?

    View Slide

  7. Is M. floridensis the parent of the asexuals?
    M. floridensis is found within
    the phylogenetic diversity
    of asexual species
    It reproduces sexually by
    automixis
    MELOIDOGYNE HYBRIDISATION GENOMICS
    M.floridensis M. ???
    M. incognita
    M. javanica
    M. arenaria
    x
    apomicts
    parental species
    automict
    apomict
    apomict
    automict

    View Slide

  8. M.floridensis M. ???
    M. incognita
    M. javanica
    M. arenaria
    x
    apomicts
    parental species
    automict
    Is M. floridensis the parent of the asexuals?
    Could it be a
    parent of the
    asexual lineages via
    interspecific
    hybridisation?
    MELOIDOGYNE HYBRIDISATION GENOMICS
    apomict
    apomict
    automict
    What can that tell us
    about the origins of
    crop pathogenicity?

    View Slide

  9. MELOIDOGYNE COMPARATIVE GENOMICS
    From Genomics to Biology
    Genomics and bioinformatics
    can reveal complex biological
    stories, and suggest novel
    approaches to agricultural
    problems

    View Slide

  10. MELOIDOGYNE HYBRIDISATION GENOMICS
    Meloidogyne comparative genomics
    We have sequenced M. floridensis
    genome and compare to 2 other
    published Meloidogyne genomes
    M.floridensis M. ???
    M. incognita
    M. javanica
    M. arenaria
    x
    apomicts
    parental species
    automict
    asexual, hybrid?
    sexual, parental?
    sexual, outgroup
    100MB, 100x coverage, 15.3k protein coding loci

    View Slide

  11. Is M. floridensis the parent of the asexuals?
    1. look at the within-genome
    patterns of diversity to
    determine hybrid nature of
    genomes
    2. look at phylogenetic
    relationships of all genes to
    study origins and parents
    MELOIDOGYNE HYBRIDISATION GENOMICS
    1: Intra-genomic diversity
    2: Phylogenomics
    Investigated using whole genome
    sequences and 2 distinct approaches;

    View Slide

  12. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    Coding sequences from each species
    were compared to loci in the same
    species
    The percent identity of the best match
    was plotted
    Self identity comparisons
    Both M. incognita and M.
    floridensis show
    evidence of presence of
    many duplicates, while
    M. hapla does not

    View Slide

  13. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    Self identity comparisons
    Both M. incognita and M.
    floridensis show
    evidence of presence of
    many duplicates, while
    M. hapla does not
    This is exactly the
    pattern expected
    for hybrid genomes

    View Slide

  14. Is M. floridensis the parent of the asexuals?
    look at phylogenetic relationships of all
    genes to study origins and parents
    MELOIDOGYNE HYBRIDISATION GENOMICS
    1: Intra-genomic diversity
    2: Phylogenomics

    View Slide

  15. Hybridisation Hypotheses
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    There are very many ways species could
    hybridise, duplicate genes, lose genes
    We have selected a broad range of
    possibilities informed by prior knowledge
    We have tested their predictions
    phylogenetically
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    A
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    C
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    D
    2. PHYLOGENOMIC ANALYSES

    View Slide

  16. 17
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    Z
    M. incognita
    Z+Z
    1 & 2
    X+Y
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    Z
    M. incognita
    +Z
    X+Y
    M. hapla
    X Y
    M. floridensis
    X+Y
    C Scenario 4
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    D
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    Hybridisation hypotheses
    A B
    C D
    We have selected a broad range of possibilities
    informed by prior knowledge
    We have tested their predictions phylogenetically

    View Slide

  17. M. hapla
    X
    M. floridensis
    X
    B Scenario
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    (A)
    Whole genome
    duplication(s)

    View Slide

  18. 19
    M. hapla
    X
    M. floridensis
    X+Y
    C Scena
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. incognita
    Z
    (B)
    M. incognita is an
    interspecific hybrid with
    M. floridensis as one
    parent

    View Slide

  19. M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y
    M. florid
    X+Y
    D Scenario
    X+Y
    (C)
    M. incognita and M.
    floridensis are
    independent hybrids
    sharing one parent

    View Slide

  20. Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    X+Y
    (D)
    M. floridensis is a hybrid
    and M. incognita is a
    secondary hybrid
    between M. floridensis and
    a 3rd parent

    View Slide

  21. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    M. hapla
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    A
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    X+Y
    C
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    X+Y
    D
    • Recover all genes from 3 genomes
    • CDS orthologues determined by InParanoid
    • 4018 ortholog clusters included all 3 species
    • Retained those with a single copy in the outgroup M. hapla
    • ML Phylogenies of relationships
    between Mi and Mf gene copies
    • Trees parsed and pooled to represent
    frequencies of different relationships

    View Slide

  22. 23
    Each tree
    contains a
    single M. hapla
    sequence as
    outgroup
    (black square)
    Grey square
    indicates
    relative
    frequency of
    those
    topologies
    Trees are
    pooled within
    squares into
    different
    patterns of
    relationships
    Grid squares
    represent
    different
    numbers of
    gene copies

    View Slide

  23. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    M. hapla
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    A
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    X+Y
    C
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    X+Y
    D
    We assess the fit of the tree topologies
    to our hypotheses
    • Five out of seven cluster sets, and 95%
    of all trees, support hybrid origins for
    both M. floridensis and M. incognita
    • ie exclude hypotheses A and B
    • Hypothesis C best explains 17 trees
    • Hypothesis D best explains 1335 trees

    View Slide

  24. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    A
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    C
    M. floridensis is a parental species
    of “double hybrid” M. incognita
    with other parent unknown
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    X+Y
    Hypothesis D
    Conclusion:

    View Slide

  25. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    Pooled analysis of ~1000 gene loci
    M. hapla
    M. incognita
    M. floridensis
    M. incognita
    Two topologies
    are present
    ‘Conflict’ is evidence
    for hybridisation

    View Slide

  26. MELOIDOGYNE COMPARATIVE GENOMICS
    From Genomics to Biology
    Genomics reveals that both
    species are hybrids and M.
    floridensis is a parent of M.
    incognita

    View Slide

  27. MELOIDOGYNE COMPARATIVE GENOMICS
    From Genomics to Biology
    Hybridisation seems common
    in this group
    Genomics reveals that both
    species are hybrids and M.
    floridensis is a parent of M.
    incognita

    View Slide

  28. MELOIDOGYNE COMPARATIVE GENOMICS
    1. Ongoing Work
    Bioinformatics pipelines for
    whole genome comparative
    analysis in nematodes

    View Slide

  29. MELOIDOGYNE COMPARATIVE GENOMICS
    1. Ongoing Work
    Genomes in a phylogenetic design
    Testing effect of recombination &
    breeding system on genome change
    • hybrids, inbred, outbred, loss of meiosis, TEs,
    mutational patterns, gene families

    View Slide

  30. MELOIDOGYNE COMPARATIVE GENOMICS
    1. Ongoing Work
    DNA
    transposons
    RNA
    transposons
    transposon evolution in Nematoda
    sequenced nematode genome

    View Slide

  31. MELOIDOGYNE COMPARATIVE GENOMICS
    1. Ongoing Work
    • Diverse sampling of most important
    species
    • Intraspecific diversity and interspecific
    divergence
    • Polymorphisms and gene loci linked to
    resistance change
    Meloidogyne diversity and adaptation to crop
    parasitism

    View Slide

  32. MELOIDOGYNE COMPARATIVE GENOMICS
    2. Future work
    • Increase sampling of Meloidogyne
    species
    • fully represent this genus
    • determine intraspecific variation
    • detect parental species
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net
    I’m happy to collaborate

    View Slide

  33. MELOIDOGYNE COMPARATIVE GENOMICS
    2. Future work
    • Functional Meloidogyne genomics
    • what is the genomic basis of
    resistance breaking lines?
    • can pathogenicity be predicted
    from genotype?
    • diagnostic tools for functional
    genomics?
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net

    View Slide

  34. MELOIDOGYNE COMPARATIVE GENOMICS
    2. Future work
    • Increase sampling of Meloidogyne species
    • What genes are associated with
    pathogenicity?
    • Adaptation to crops through transgressive
    segregation?
    • The ‘hybrid threat’
    • Other nematode species
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net

    View Slide

  35. MELOIDOGYNE COMPARATIVE GENOMICS
    2. Future work
    • Transgressive segregation and polyphagy
    • testing transgressive segregation
    • genome reorganisation in hybridogenesis
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net

    View Slide

  36. ADAPTATION TO THE AGRICULTURAL ENVIRONMENT
    Transgressive segregation
    Transgressive segregation is when the absolute values
    of traits in some hybrids exceed the trait variation
    shown by either parental lineage
    Hybrid
    Parent 1 Parent 2
    Arrows represent ‘phenotypic range’

    View Slide

  37. MELOIDOGYNE COMPARATIVE GENOMICS
    2. Future work
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net
    Question
    If hybridisation can lead to extreme
    polyphagy and crop pathogenicity,
    do we need to monitor the “hybrid
    threat”?
    speakerdeck.com/davelunt
    slides available

    View Slide

  38. MELOIDOGYNE COMPARATIVE GENOMICS
    Root Knot Nematode Genomes
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net
    speakerdeck.com/davelunt
    slides available

    View Slide