GLOBALLY IMPORTANT CROP PESTS AMIR SZITENBERG, LAURA SALAZAR, VIVIAN BLOK, SOUMI JOSEPH, DOMINIK LAETSCH, VALERIE WILLIAMSON, MARK BLAXTER, DAVE LUNT @davelunt [email protected] speakerdeck.com/davelunt slides:
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 most of this work
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
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
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
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
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
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 [email protected] speakerdeck.com/davelunt slides available metadata; know your enemy data accession: PRJNA340324 both raw data and genome assemblies