Meloidogyne comparative genomics

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

Transcript

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
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