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Meloidogyne comparative genomics

96e8ca061c005a42d360459d366ec923?s=47 Dave Lunt
September 01, 2016

Meloidogyne comparative genomics

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

96e8ca061c005a42d360459d366ec923?s=128

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 davelunt@gmail.com speakerdeck.com/davelunt slides:
  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 davelunt@gmail.com speakerdeck.com/davelunt slides available data accession: PRJNA340324 Amir Szitenberg & Laura Salazar have carried out most of this work
  3. None
  4. 18S structural alignment ML tree

  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
  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
  7. MITOCHONDRIAL GENOME PHYLOGENY MIG species are resolved by mtDNA Close

    relatives; they show very little divergence Concatenated genes, ML tree, RAxML MIG
  8. NUCLEAR GENOMES GENOMES ARE COMPLEX, CONTAINING TWO DIVERGENT GENOME COPIES

    ORTHOLOGOUS LOCI MUST BE CORRECTLY IDENTIFIED
  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
  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
  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
  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
  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
  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
  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
  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 davelunt@gmail.com speakerdeck.com/davelunt slides available metadata; know your enemy data accession: PRJNA340324 both raw data and genome assemblies
  17. None