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

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 WHAT’S IN A GENOME & WHY? HeLa cell nuclei BRIEFLY HOW DO THE EVOLUTIONARY FORCES DETERMINE THE SHAPE AND CONTENT OF OUR GENOMES? MUTATION, SELECTION, DRIFT, GENE FLOW, AND RECOMBINATION Evolutionary forces

JD Eisenback onion, Allium cepa 15 GB genome nematode, Meloidogyne sp 150 MB genome = 1% onion infected uninfected

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

GLOBALLY IMPORTANT CROP PESTS ROOT-KNOT NEMATODES genus Meloidogyne ENORMOUS PLANT HOST RANGE ~5% LOSS IN WORLD AGRICULTURE? ALL MAJOR CROPS SPECIES 6 den Akker SE, Jones JT. doi:10.1371/journal.pgen.1007160 M. incognita parasitises the majority of flowering plant diversity, red

“M. INCOGNITA IS FOUND IN EVERY COUNTRY WITH A LOWEST TEMPERATURE >3±C, & IS POSSIBLY THE SINGLE MOST DAMAGING CROP PATHOGEN IN THE WORLD. IN ECUADOR, BASED ON A SURVEY OF 207 HORTICULTURAL CROPS, ESTIMATED LOSSES DUE TO M. INCOGNITA EXCEED 20%” 7 den Akker SE, Jones JT. doi:10.1371/journal.pgen.1007160 Trudgill and Blok 2001 Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. doi:10.1146/annurev.phyto.39.1.53

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9 MIG are the tropical root-knot nematodes, causing major economic loss THE MELOIDOGYNE INCOGNITA GROUP THE MIG OUTGROUP

10 MELOIDOGYNE INCOGNITA GROUP ARE 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

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 11 RKN juveniles SEX REFERS TO MEIOSIS NOT MATING

12 RKN female SEM overlaid with juveniles WIDE VARIETY OF REPRODUCTIVE MODES IN SINGLE GENUS 18S structural alignment ML tree The genus has >6 losses of meiosis and many other transitions Janssen et al 2017 doi:10.1371/journal.pone.0172190, Lunt unpublished

13 RKN female SEM overlaid with juveniles WIDE VARIETY OF REPRODUCTIVE MODES IN SINGLE GENUS 18S structural alignment ML tree Frequent reproductive mode changes gives opportunity to examine evolutionary genomics of meiosis Work ongoing

Szitenberg et al Genome Biology & Evolution 2016 doi:10.1093/gbe/evw208 DNA TEs LTRs transposons 500 million years of evolution 42 genomes 14 NEMATODE TRANSPOSABLE ELEMENTS FOLLOW PHYLOGENY THE GENOMIC TRANSPOSABLE ELEMENT LOAD IS EXPLAINED BY PHYLOGENY NOT BREEDING SYSTEM

ASEXUAL ORGANISMS CAN ADAPT RAPIDLY & COMPETE SUCCESSFULLY DO NOT BE DISTRACTED BY ‘TABLOID’ SCIENTIFIC SEX STORIES ASEXUAL ROOT-KNOT NEMATODES ARE EXCEPTIONALLY SUCCESSFUL, RAPIDLY ADAPTING, AND NOT SUFFERING FROM ACCUMULATION OF DELETERIOUS GENOMIC MUTATIONS

HOW CAN WE APPLY NEMATODE GENOMICS & BIOINFORMATICS FOR SUSTAINABLE AGRICULTURE? INCREASING CHALLENGES FOR SUSTAINABLE AGRICULTURE

‘WHOEVER COULD MAKE TWO EARS OF CORN, OR TWO BLADES OF GRASS, TO GROW UPON A SPOT OF GROUND WHERE ONLY ONE GREW BEFORE, WOULD DESERVE BETTER OF MANKIND… THAN THE WHOLE RACE OF POLITICIANS PUT TOGETHER’ “GULLIVER’S TRAVELS” 1726, BY JONATHAN SWIFT

WHY EVOLUTIONARY COMPARATIVE GENOMICS? WHATS THE POINT OF ALL THIS?

KNOW YOUR ENEMY! WHATS THE POINT OF ALL THIS? Root-knot nematode J2 juveniles swarming before attack

GENOMICS AND BIOINFORMATICS CAN REVEAL COMPLEX BIOLOGICAL STORIES THIS UNDERSTANDING SUGGESTS NOVEL APPROACHES TO AGRICULTURAL PROBLEMS

IMPORTANT GENOMICS PAPERS TELL THE SAME STORY 2008 2008 2017 2017 2014

22 Szitenberg et al. Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol. 2017;9: 2844–2861. doi:10.1093/gbe/evx201 WE HAVE SEQUENCED 19 NEW GENOMES Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EGJ, Deleury E, et al. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. 2008;26: 909–915. doi:10.1038/ nbt.1482 Lunt DH. Genetic tests of ancient asexuality in root knot nematodes reveal recent hybrid origins. BMC Evol Biol. 2008;8: 194. doi:10.1186/1471-2148-8-194 Lunt DH, Kumar S, Koutsovoulos G, Blaxter ML. The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PeerJ. PeerJ Inc.; 2014;2: e356. doi:10.7717/peerj.356 Blanc-Mathieu R, Perfus-Babeoch L, Aury J-M, Da Rocha M, Gouzy J, Sallet E, et al. Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis [Internet]. bioRxiv. 2016. p. 046805. doi:10.1101/046805

NERC, AFRICA GOMEZ, CHARLES OPPERMAN, DAVID BIRD, ETIENNE DANCHIN, PHILIPPE CASTAGNONE- SERENO, BOB ROBBINS, PABLO CASTILLO & MANY MANY OTHERS 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 Szitenberg et al. Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol. 2017;9: 2844–2861. doi:10.1093/gbe/evx201

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

Apomicts M. floridensis M. hapla M. chitwoodi M. incognita M. javanica M. arenaria INTRA-GENOMIC BLAST ANALYSIS 25 Most genes have another copy about 3% divergent mitotic parthenogens

ABOUT HALF OF APOMICT GENOMES HAVE A DIVERGENT COPY Number of Orthology Groups M. incognita M. javanica M. arenaria M. floridensis Copies per genome has mostly lost the divergent second genome copy 26 but M. floridensis is mostly homozygous

27 NUCLEAR PHYLOGENOMICS RESOLVES THE RELATIONSHIPS M. floridensis M. incognita M. arenaria M. javanica Libya USA French West Indies Ivory Coast USA Morocco French West Indies USA

PHYLOGENOMICS OF 2 DIVERGENT GENOME COPIES 533 Ortholog CDS supermatrix ML tree RAxML B A 28 M. floridensis M. incognita M. arenaria M. javanica M. enterolobii M. floridensis M. incognita M. arenaria M. javanica

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 B A 29

PHYLOGENOMICS OF 2 DIVERGENT GENOME COPIES 533 Ortholog CDS supermatrix ML tree RAxML M. floridness is a sibling not a parent of the apomicts M. incognita M. javanica M. arenaria M. floridensis B A 30 No species contains 3 genomic copies, indicating a single hybridisation Mf Mf

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?

ADAPTATION TO AGRICULTURAL ENVIRONMENT INTERSPECIFIC HYBRIDISATION IS 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 APOMICTS ARE VERY HETEROZYGOUS, VERY POLYPHAGOUS, VERY ADAPTABLE

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 33

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 OTHER POLICY LEVELS EXIST

35 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

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

GENE CONVERSION IS AN IMPORTANT FORCE SHAPING THE APOMICT GENOMES THERE IS EVIDENCE OF GENE CONVERSION BUT NOT HOMOLOGOUS-EXCHANGE RECOMBINATION GENE CONVERSION MAY BE A SOURCE OF ADAPTIVE VARIATION

38 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 We do not observe this process This is frequent Szitenberg et al. Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol. 2017;9: 2844–2861. doi:10.1093/gbe/evx201

Blanc-Mathieu et al. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genet. Public Library of Science; 2017;13: e1006777. Available: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006777 Figure S3 BOTH SZITENBERG ET AL AND BLANC-MATHIEU ET AL FIND A MIXTURE OF DIVERGENT AND INVARIANT SEQUENCE ON LONG CONTIGS Is this gene conversion? Chromosomes may be patchworks of the former A and B parental genomes

ABOUT HALF OF APOMICT GENOMES HAVE A DIVERGENT COPY Number of Orthology Groups M. incognita M. javanica M. arenaria M. floridensis Copies per genome has mostly lost the divergent second genome copy 40 but M. floridensis is mostly homozygous

SUMMARY GENOMIC COMPLEXITY 41 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

FUTURE QUESTIONS 42 CAN WE LOCATE FUNCTIONAL LOCI FOR VIRULENCE AVIRULENCE? WHAT IS THE NATURE OF THE ADAPTIVE VARIATION? DO GENOME COPIES FULFIL THE SAME ROLES?

43 VERY LITTLE GENETIC DIVERGENCE GLOBALLY YET… THERE ARE VIRULENCE DIFFERENCES BETWEEN ISOLATES Are SNPs surveying the true genomic basis of phenotypic change? QUESTION

GENOMICS HAS ONLY SCRATCHED THE SURFACE OF ROOT-KNOT DIVERSITY 44 WHAT ARE THE PARENTAL SPECIES? WHAT IS THE SOURCE COUNTRY OF APOMICTS?

FUTURE ACTIONS BROADEN THE NUMBER OF SPECIES SAMPLED METADATA COLLECTION WITH GENOMES INDUSTRIAL AND ACADEMIC COLLABORATION CHARACTERISE MUCH MORE GENOMIC INTRASPECIFIC VARIATION 45 WHAT IF…. HIGH QUALITY REFERENCE GENOMES

WHAT IF BOTH CROP ISOLATE AND NEMATODE 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

WHAT IF WE COULD GET SINGLE INDIVIDUAL RKN GENOME-BASED DIAGNOSTIC OF LIKELY HOST RANGE AND CROP THREAT? RKN female JD Eisenback

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