Root Knot Nematode Comparative Genomics

Transcript

1. ROOT-KNOT NEMATODE
   COMPARATIVE GENOMICS
   UNDERSTANDING EVOLUTION,
   DIVERSITY AND THREAT
   EVOHULL: EVOLUTIONARY AND ENVIRONMENTAL GENOMICS
   UNIVERSITY OF HULL, UK
   @davelunt
   davelunt@gmail.com davelunt.net
   Dr Dave Lunt
   

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2. EVOHULL: EVOLUTIONARY AND ENVIRONMENTAL GENOMICS
   UNIVERSITY OF HULL, UK
   @davelunt
   davelunt@gmail.com davelunt.net
   Dr Dave Lunt
   invasive species
   ecological networks in forestry and agriculture
   biomonitoring bioinformatics
   metabarcoding genomics
   phylogenetics
   apomixis and breeding systems
   environmental DNA
   

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3. ROOT-KNOT NEMATODE
   COMPARATIVE GENOMICS
   UNDERSTANDING EVOLUTION,
   DIVERSITY AND THREAT
   EVOHULL: EVOLUTIONARY AND ENVIRONMENTAL GENOMICS
   UNIVERSITY OF HULL, UK
   @davelunt
   davelunt@gmail.com davelunt.net
   Dr Dave Lunt
   

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4. NERC, AFRICA GOMEZ, CHARLES
   OPPERMAN, DAVID BIRD, ETIENNE
   DANCHIN, PHILIPPE CASTAGNONE-
   SERENO, BOB ROBBINS, PABLO
   CASTILLO & MANY MANY OTHERS
   @davelunt
   davelunt@gmail.com
   data accession: PRJNA340324
   Amir Szitenberg & Laura Salazar have carried out much of this work
   AMIR SZITENBERG, LAURA SALAZAR, VIVIAN BLOK, SOUMI JOSEPH, DOMINIK
   LAETSCH, VALERIE WILLIAMSON, MARK BLAXTER, DAVE LUNT
   THANKS
   images: Wikipedia, JD Eisenback, et al
   

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5. 5
   WHAT’S IN A
   GENOME & WHY?
   RESEARCH QUESTION 1
   HeLa cell nuclei
   

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6. Marbled lungfish ~133 Gbp
   Pratylenchus coffeae,
   Plant-parasitic nematode
   ~20Mb
   1/6,650
   

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7. Bear garlic Allium ursinum
   31.5 GB genome
   Chives, Allium schoenoprasum
   7 GB genome
   Ricroch et al. Evolution of genome size across some cultivated
   Allium species. Genome. 2005;48: 511–520. doi:10.1139/g05-017
   1/4.5
   

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8. onion, Allium cepa
   15 GB genome
   human, Homo sapiens
   3 GB genome
   

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9. JD Eisenback
   onion, Allium cepa
   15 GB genome
   nematode, Meloidogyne sp
   150 MB genome
   infected
   uninfected
   

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10. MOSTLY TRANSPOSONS,
    REPEATS, AND SEQUENCES OF
    UNKNOWN ORIGIN
    WHAT’S IN A GENOME?
    BUT WHY?
    onion, Allium cepa
    15 GB genome
    human, Homo sapiens
    3 GB genome
    

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11. RECOMBINATION
    GENE FLOW
    GENETIC DRIFT
    MUTATION
    SELECTION
    EVOLUTIONARY FORCES
    WHY IS GENOME CONTENT AS IT IS?
    

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12. TRANSPOSABLE
    ELEMENTS IN
    THE NEMATODA
    42 GENOMES
    500 MILLION YEARS
    OF EVOLUTION
    Szitenberg et al Genome Biology & Evolution 2016
    doi:10.1093/gbe/evw208
    

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13. Szitenberg et al Genome Biology & Evolution 2016 doi:10.1093/gbe/evw208
    DNA TEs LTRs
    transposons
    500 million years of evolution 42 genomes
    13
    NEMATODE TRANSPOSABLE ELEMENTS FOLLOW PHYLOGENY
    THE GENOMIC TRANSPOSABLE ELEMENT LOAD IS EXPLAINED BY
    PHYLOGENY NOT BREEDING SYSTEM
    

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14. HOW CAN WE APPLY
    GENOMICS &
    BIOINFORMATICS FOR
    SUSTAINABLE AGRICULTURE?
    RESEARCH QUESTION 2
    

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15. GLOBALLY IMPORTANT CROP PESTS
    ROOT-KNOT NEMATODES genus Meloidogyne
    ENORMOUS PLANT HOST RANGE
    ~5% WORLD AGRICULTURE?
    ALL MAJOR CROPS SPECIES
    15
    

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17. WIDE VARIETY OF REPRODUCTIVE MODES IN SINGLE GENUS
    ▸ Asexual (mitotic)
    ▸ mitotic parthenogenesis- apomixis
    ▸ no meiosis or exchange
    ▸ Sexual (meiotic)
    ▸ meiotic parthenogenesis- automixis
    ▸ outbreeding sexuality- amphimixis
    ▸ meiosis and genetic exchange
    17
    RKN juveniles
    

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18. 18
    RKN female SEM overlaid
    with juveniles
    WIDE VARIETY OF REPRODUCTIVE MODES IN SINGLE GENUS
    18S structural alignment ML tree
    Reproductive
    mode changes
    frequently within
    the genus
    

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19. 19
    RKN female SEM overlaid
    with juveniles
    WIDE VARIETY OF REPRODUCTIVE MODES IN SINGLE GENUS
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    

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20. 20
    RKN female SEM overlaid
    with juveniles
    WIDE VARIETY OF REPRODUCTIVE MODES IN SINGLE GENUS
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    THE GENUS HAS >6
    TRANSITIONS TO MITOTIC
    PARTHENOGENESIS
    LOSS OF SEX/MEIOSIS
    FACULTATIVE MEIOTIC
    PARTHENOGENESIS (AUTOMIXIS)
    AND SEXUALITY (AMPHIMIXIS)
    

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21. 21
    RKN female SEM overlaid
    with juveniles
    TAXONOMY AND CROP DAMAGE: THE TROPICAL APOMICTS
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    

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22. 22
    RKN female SEM overlaid
    with juveniles
    TAXONOMY AND CROP DAMAGE: THE TROPICAL APOMICTS
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    

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23. 23
    RKN female SEM overlaid
    with juveniles
    TAXONOMY AND CROP DAMAGE: THE TROPICAL APOMICTS
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    

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24. 24
    ALL APOMICTS EXCEPT M. FLORIDENSIS
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    These are the tropical root-knot nematodes,
    causing major economic loss
    

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25. 25
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    These are the tropical root-knot nematodes,
    causing major economic loss
    THE MELOIDOGYNE INCOGNITA GROUP
    THE MIG
    OUTGROUP
    

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26. 26
    Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
    These are the tropical root-knot nematodes,
    causing major economic loss
    THE MELOIDOGYNE INCOGNITA GROUP
    THE MIG
    OUTGROUP
    We have genome sequenced
    19 new genomes
    

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27. GENOMICS AND
    BIOINFORMATICS CAN REVEAL
    COMPLEX BIOLOGICAL
    STORIES, AND SUGGEST NOVEL
    APPROACHES TO
    AGRICULTURAL PROBLEMS
    

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28. GENOMICS AND BIOINFORMATICS
    ▸Phylogeny and diversity
    ▸Genome structure
    ▸Origins and speciation
    ▸Hybrids?
    ▸Polyploids?
    28
    

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29. 29
    SMALL MTDNA DIVERGENCES
    Edinburgh Genomics
    mtDNA genome phylogeny
    mtDNA is a poor
    diagnostic tool
    

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30. 30
    SMALL MTDNA DIVERGENCES
    mtDNA genome phylogeny Edinburgh Genomics
    

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31. MIG GENOMES ARE HYBRID,
    COMPLEX, AND CONTAIN
    TWO GENOMIC COPIES
    UNDERSTANDING THE COMPLEXITY
    WILL INFORM BIOLOGY AND CONTROL
    Lunt et al. 2014 The complex hybrid origins of the root knot nematodes revealed through comparative genomics. doi:10.7717/peerj.356
    

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32. Apomicts
    M. floridensis
    M. hapla M. chitwoodi
    M. incognita
    M. javanica
    M. arenaria
    INTRA-GENOMIC BLAST ANALYSIS
    32
    

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33. MOST MIG GENOMES HAVE A MIX OF DIVERGENT
    AND HOMOZYGOUS REGIONS
    Number of Orthology Groups
    M. incognita M. javanica
    M. arenaria
    M. floridensis
    Copies per genome
    has mostly lost the
    divergent second
    genome copy
    33
    

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34. PHYLOGENOMICS OF 2 DIVERGENT GENOME COPIES
    533 Ortholog CDS supermatrix ML tree RAxML
    Single origin of 2 genome
    copies predating speciation
    Phylogeny in each genome
    copy A/B is identical
    M. incognita M. javanica M. arenaria M. floridensis
    colours are different species not reproductive system
    B
    A
    34
    

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35. 35
    NUCLEAR PHYLOGENOMICS RESOLVES THE RELATIONSHIPS
    M. floridensis
    M. incognita
    M. arenaria
    M. javanica
    

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36. 36
    VERY LITTLE GENETIC DIVERGENCE GLOBALLY
    M. floridensis
    M. incognita
    M. arenaria
    M. javanica
    Libya
    USA
    French West Indies
    Ivory Coast
    USA
    Morocco
    French West Indies
    USA
    ROOT-KNOT NEMATODES LIKELY SPREAD WITH MODERN AGRICULTURE
    

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37. Eisenback and Triantaphyllou 1991
    37
    

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38. ADAPTATION TO AGRICULTURAL ENVIRONMENT
    ONCE THOUGHT THAT HYBRID
    SPECIATION WAS RARE AND
    INCONSEQUENTIAL IN ANIMALS Heliconius
    Lake Malawi
    Polar and brown
    GENOME BIOLOGY IS
    REVEALING A VERY DIFFERENT
    VIEW
    HYBRID SPECIATION IN MELOIDOGYNE?
    

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39. ADAPTATION TO AGRICULTURAL ENVIRONMENT
    PREVIOUS WORK
    SUGGESTS INTERSPECIFIC
    HYBRIDISATION MAY BE
    INVOLVED WITH
    MELOIDOGYNE ASEXUAL
    SPECIES
    Heliconius butterflies
    Lake Malawi cichlids
    Root knot nematodes?
    HYBRID SPECIATION IN MELOIDOGYNE?
    Lunt et al. 2014 The complex hybrid origins of the root knot nematodes revealed through comparative genomics.
    doi:10.7717/peerj.356
    

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40. X
    parent 1 parent 2
    hybrid offspring phenotypic variation
    parental phenotypic variation
    TRANSGRESSIVE SEGREGATION
    phenotype could be anything, including nematode host-range
    is greater than sum of parental variation
    Transgressive segregation is when the absolute values of traits in some hybrids exceed the trait variation shown by either parental lineage
    small big
    very small very big
    40
    

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41. THE APOMICTS ARE
    HYPO-TRIPLOID
    SOME REGIONS OF THE APOMICTS
    ARE PRESENT IN 3 COPIES A1,A2,B
    hypo-triploid = not full triploid, some parts of genome are diploid
    

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42. 42
    TROPICAL APOMICTS ARE HYPO-TRIPLOIDS
    hypo-triploid = not full triploid, some parts of genome are diploid
    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
    

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43. TROPICAL APOMICTS ARE HYPO-TRIPLOIDS
    read depth analysis demonstrates hypo-triploidy
    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 high quality PacBio genome
    copy A1 copy B
    copy A2
    copy number
    1
    2
    sequence read depth
    A + B
    

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44. GENE CONVERSION IS AN
    IMPORTANT FORCE SHAPING
    THE APOMICT GENOMES
    THERE IS EVIDENCE OF GENE CONVERSION BUT
    NOT HOMOLOGOUS-EXCHANGE RECOMBINATION
    

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45. 45
    NO EVIDENCE OF RECIPROCAL EXCHANGE
    AMONG APOMICTS
    GENE CONVERSION IS EVIDENT
    RECIPROCAL EXCHANGE GENE CONVERSION
    A1 B
    A2 A1 B
    A2
    Identical & no recombination detectable
    B
    A1
    A2
    or
    

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46. SUMMARY
    46
    GENOMES CONTAIN DIVERGENT A AND B COPIES
    MIG APOMICTS ARE HYPOTRIPLOID
    A AND B DIVERGED BEFORE MIG SPECIES
    GENE CONVERSION IS A POWERFUL FORCE
    MIG ARE DIVERGENT DUE TO MUCH MORE
    THAN SIMPLE MUTATION
    NUCLEAR GENOME RESOLVES PHYLOGENY
    

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47. FUTURE QUESTIONS
    47
    CAN WE LOCATE FUNCTIONAL LOCI FOR VIRULENCE AVIRULENCE?
    WHAT IS THE NATURE OF THE ADAPTIVE VARIATION?
    HAVE MIG OUTRUN THEIR PATHOGENS?
    DO GENOME COPIES FULFIL THE SAME ROLES?
    

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48. GENOMICS HAS ONLY SCRATCHED THE
    SURFACE OF ROOT-KNOT DIVERSITY
    48
    

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49. GENOMICS HAS ONLY SCRATCHED THE
    SURFACE OF ROOT-KNOT DIVERSITY
    49
    

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50. FUTURE ACTIONS
    BROADEN THE NUMBER OF SPECIES SAMPLED
    METADATA COLLECTION WITH GENOMES
    INDUSTRIAL AND ACADEMIC COLLABORATION
    CHARACTERISE MUCH MORE GENOMIC INTRASPECIFIC VARIATION
    50
    WHAT IF….
    

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51. WHAT IF BOTH CROP ISOLATE AND
    NEMATODE RACE GENOMES WERE
    KNOWN?
    By Mason Masteka - originally posted to Flickr as End of Summer Tomatoes, CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=11444911
    

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52. WHAT IF WE COULD MOVE FROM
    SINGLE INDIVIDUAL RKN TO GENOME-
    BASED DIAGNOSTIC OF LIKELY HOST
    RANGE AND CROP THREAT?
    JD Eisenback
    

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53. ROOT-KNOT NEMATODE
    COMPARATIVE GENOMICS
    UNDERSTANDING EVOLUTION,
    DIVERSITY AND THREAT
    Dr Dave Lunt
    EVOHULL: EVOLUTIONARY AND ENVIRONMENTAL GENOMICS
    UNIVERSITY OF HULL, UK
    @davelunt
    davelunt@gmail.com davelunt.net
    By Mason Masteka - originally posted to Flickr as End of Summer Tomatoes, CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=11444911
    

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54. Root-Knot Nematodes Meloidogyne spp
    

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