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

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

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

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

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

   HeLa cell nuclei

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

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

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

   GB genome

9. JD Eisenback onion, Allium cepa 15 GB genome nematode, Meloidogyne

   sp 150 MB genome infected uninfected

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

11. RECOMBINATION GENE FLOW GENETIC DRIFT MUTATION SELECTION EVOLUTIONARY FORCES WHY

    IS GENOME CONTENT AS IT IS?

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

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

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

    RESEARCH QUESTION 2

15. GLOBALLY IMPORTANT CROP PESTS ROOT-KNOT NEMATODES genus Meloidogyne ENORMOUS PLANT

    HOST RANGE ~5% WORLD AGRICULTURE? ALL MAJOR CROPS SPECIES 15
16. None

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

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

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

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)

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

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

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

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

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

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

27. GENOMICS AND BIOINFORMATICS CAN REVEAL COMPLEX BIOLOGICAL STORIES, AND SUGGEST

    NOVEL APPROACHES TO AGRICULTURAL PROBLEMS

28. GENOMICS AND BIOINFORMATICS ▸Phylogeny and diversity ▸Genome structure ▸Origins and

    speciation ▸Hybrids? ▸Polyploids? 28

29. 29 SMALL MTDNA DIVERGENCES Edinburgh Genomics mtDNA genome phylogeny mtDNA

    is a poor diagnostic tool

30. 30 SMALL MTDNA DIVERGENCES mtDNA genome phylogeny Edinburgh Genomics

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

32. Apomicts M. floridensis M. hapla M. chitwoodi M. incognita M.

    javanica M. arenaria INTRA-GENOMIC BLAST ANALYSIS 32

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

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

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

    M. arenaria M. javanica

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

37. Eisenback and Triantaphyllou 1991 37

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?

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

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

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

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

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

44. GENE CONVERSION IS AN IMPORTANT FORCE SHAPING THE APOMICT GENOMES

    THERE IS EVIDENCE OF GENE CONVERSION BUT NOT HOMOLOGOUS-EXCHANGE RECOMBINATION

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

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

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?

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

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

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….

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

52. WHAT IF WE COULD MOVE FROM SINGLE INDIVIDUAL RKN TO

    GENOME- BASED DIAGNOSTIC OF LIKELY HOST RANGE AND CROP THREAT? JD Eisenback

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

54. Root-Knot Nematodes Meloidogyne spp