COMPARATIVE GENOMICS OF SEXUAL AND ASEXUAL NEMATODES- ORIGINS, PLOIDY, AND MOLECULAR EVOLUTION @davelunt [email protected] speakerdeck.com/davelunt slides: Dave Lunt EvoHull Evolutionary Genomics Group, University of Hull Blaxter Lab, University of Edinburgh

THANKS: NERC, AFRICA GOMEZ, CHARLES OPPERMAN, DAVID BIRD, ETIENNE DANCHIN, PHILIPPE CASTAGNONE-SERENO, BOB ROBBINS, PABLO CASTILLO & MANY MANY OTHERS @davelunt [email protected] speakerdeck.com/davelunt slides available 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 ROOT KNOT NEMATODE COMPARATIVE GENOMES

Infected Uninfected Root Knot Nematodes, genus Meloidogyne

18S structural alignment ML tree Reproductive mode changes frequently within the genus

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

GENOMES OF THE MAIN AGRICULTURAL PATHOGENS M. arenaria M. javanica M. incognita M. floridensis M. enterolobii M. haplanaria 3 genomes 5 genomes 8 genomes 1 genome 2 genomes 1 genome

INTRASPECIFIC BLAST SHOWS 2 DIVERGENT GENOME COPIES divergence of copy A and copy B ~3% in protein coding regions no divergent genomic copies Automict outgroups Automict Apomicts Apomict

PHYLOGENOMICS OF 2 DIVERGENT GENOME COPIES 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 A B Orthologue CDS supermatrix ML tree RAxML colours are different species not reproductive system

annotated genes mostly Stacked bar charts representing estimated genome size and content unannotated Intergenic DNA Repetitive elements SSRs Transposons homozygous APOMICTS ARE HYPOTRIPLOIDS B A A1 A2 B A1 A2 B A1 A2 B & Outgroups Automict Apomict Apomict Apomict HYPOTRIPLOID = not full triploid, some parts of genome are diploid 70 70 10 Mb 10 80 80 60 60 40 60 60

HYPOTRIPLOID 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

READ DEPTH ANALYSIS DEMONSTRATES HYPOTRIPLOIDY 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 high quality PacBio genome copy A1 copy B copy A2 copy number 1 2 sequence read depth A + B

RECOMBINATION TESTS NO EVIDENCE OF RECIPROCAL EXCHANGE IN APOMICTS GENE CONVERSION IS EVIDENT RECIPROCAL EXCHANGE GENE CONVERSION A1 B A2 A1 B A2 Identical & no recombination detectable B A1 A2

INTRASPECIFIC BLAST SHOWS 2 DIVERGENT GENOME COPIES Apomicts Automict Automict outgroups Lower proportion of genome A+B due to gene conversion? Question:

GENOMES OF SEXUAL AND ASEXUAL NEMATODES ARE VERY SIMILAR

POPULATION GENOMICS OF REPRODUCTIVE MODE CHANGE IS COMPLEX AND DIVERSE How many phylogenetically independent contrasts? Long term evolution effects Power? Taxonomically narrow systems? Null hypothesis? Experimenter degrees of freedom? Phylogenetically controlled design? gene conversion and parasexual processes Note to self: must not rant against other study designs

The genomic transposable element load is explained by phylogeny not breeding system NEMATODA TRANSPOSABLE ELEMENTS FOLLOW PHYLOGENY Szitenberg et al Genome Biology & Evolution 2016 doi:10.1093/gbe/evw208 DNA TEs LTRs transposons 500 million years of evolution 42 genomes Analyses and scripts DOI: 10.5281/zenodo.58256

A COMMUNITY FOR REPRODUCIBLE POPULATION GENOMICS OPEN DATA SHARING & REPRODUCIBILITY Better science will be done, and more problems will be solved, with data freely and immediately available to all Open standards, sharing, & reproducible analysis pipelines will benefit all @davelunt [email protected] speakerdeck.com/davelunt slides available data accession: PRJNA340324 both raw data and genome assemblies THANK YOU, QUESTIONS?