Sujai Kumar Comparative genomics of root knot nematodes: Tales of sex, hybridisation and adaptation Evolutionary Biology Group, University of Hull Institute of Evolutionary Biology, University of Edinburgh
without chromosome pairs. Ancient asexuals? Asexuals- meiosis absent • Meiotic parthenogens (automixis) • Obligatory outbreeding sexuals with males & females (amphimixis) Sexuals- meiosis present Wide variety of reproductive modes in a single genus
is found within the phylogenetic diversity of asexual species! It reproduces sexually by automixis! Could it be a parent of the asexual lineages via interspecific hybridisation? MELOIDOGYNE HYBRIDISATION GENOMICS M.floridensis M. ??? M. incognita M. javanica M. arenaria x apomicts parental species automict apomict apomict automict
floridensis genome and compare to 2 other published Meloidogyne genomes M.floridensis M. ??? M. incognita M. javanica M. arenaria x apomicts parental species automict asexual, hybrid? sexual, parental? sexual, outgroup 100MB, 100x coverage, 15.3k protein coding loci
at the within-genome patterns of diversity to determine hybrid nature of genomes! 2. look at phylogenetic relationships of all genes to study origins and parents MELOIDOGYNE HYBRIDISATION GENOMICS 1: Intra-genomic diversity 2: Phylogenomics Investigated using whole genome sequences and 2 distinct approaches;
arXiv 2013 http://arxiv.org/abs/1306.6163 Coding sequences from each species were compared to loci in the same species! The percent identity of the best match was plotted Self identity comparisons Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
arXiv 2013 http://arxiv.org/abs/1306.6163 Self identity comparisons Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not This is exactly the pattern expected for hybrid genomes
X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 Z M. incognita Z+Z 1 & 2 X+Y M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 Z M. incognita +Z X+Y M. hapla X Y M. floridensis X+Y C Scenario 4 M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla D M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 Hybridisation hypotheses A B C D We have selected a broad range of possibilities informed by prior knowledge! We have tested their predictions phylogenetically
2013 http://arxiv.org/abs/1306.6163 M. hapla M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 A M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 B M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 X+Y C M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 X+Y D • Recover all genes from 3 genomes! • CDS orthologues determined by InParanoid! • 4018 ortholog clusters included all 3 species! • Retained those with a single copy in the outgroup M. hapla ! • ML Phylogenies of relationships between Mi and Mf gene copies! • Trees parsed and pooled to represent frequencies of different relationships
outgroup (black square) Grey square indicates relative frequency of those topologies Trees are pooled within squares into different patterns of relationships Grid squares represent different numbers of gene copies
2013 http://arxiv.org/abs/1306.6163 M. hapla M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 A M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 B M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 X+Y C M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 M. hapla X Z M. floridensis M. incognita X X+Z B Scenario 3 M. hapla X Z M. floridensis M. incognita X Z+Z A Scenario 1 & 2 X+Y D We assess the fit of the tree topologies to our hypotheses! • Five out of seven cluster sets, and 95% of all trees, support hybrid origins for both M. floridensis and M. incognita! • ie exclude hypotheses A and B! • Hypothesis C best explains 17 trees! • Hypothesis D best explains 1335 trees
2013 http://arxiv.org/abs/1306.6163 M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z M. hapla X Z M. floridensis M. incognita X X+Z M. hapla X Z M. floridensis M. incognita X Z+Z X+Y A M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z M. hapla X Z M. floridensis M. incognita X X+Z M. hapla X Z M. floridensis M. incognita X Z+Z X+Y B M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z M. hapla X Z M. floridensis M. incognita X X+Z M. hapla X Z M. floridensis M. incognita X Z+Z X+Y C M. floridensis is a parental species of “double hybrid” M. incognita with other parent unknown M. hapla X Y Z M. floridensis M. incognita X+Y Y+Z C Scenario 4 M. hapla X Y Z M. floridensis M. incognita X+Y (X+Y)+Z D Scenario 5 X Z M. floridensis M. incognita X X+Z B Scenario 3 X+Y Hypothesis D Conclusion:
phylogenetic design! • Testing effect of recombination & breeding system on genome change! • hybrids, inbred, outbred, loss of meiosis, TEs, mutational patterns, gene families Meloidogyne breeding system and genome evolution
the bar…! • ancient asexuality! • reproductive mode transitions! • adaptation through transgressive segregation! • the ‘hybrid threat’! • distinguishing single/multiple origins of apomicts! • contagious asexuality Dave Lunt Evolutionary Biology Group, University of Hull [email protected] davelunt.net speakerdeck.com/davelunt slides available
Sujai Kumar Comparative genomics of root knot nematodes: Tales of sex, hybridisation and adaptation Evolutionary Biology Group, University of Hull Institute of Evolutionary Biology, University of Edinburgh [email protected] davelunt.net