Le lundi 21 février, à 11h00, salle de conférences du Caren, UR1, Beaulieu.
Le lundi 21 février, à 11h00
, salle de conférences du Caren, UR1, Beaulieu.
Evolution after genome duplication
You are an octoploid. Due to two rounds of whole genome duplication (R1, R2) at the base of vertebrate phylogeny, the haploid human genome has four copies of many genes present in single copy in an ancestor to vertebrates. Subsequent to R2, teleost fish experienced an additional round of genome duplication, the teleost genome duplication (R3 or TGD), and later still, salmonids suffered a fourth round of genome duplication (R4 or SGD). To understand the principles by which duplicated genes evolved after R1 and R2 and now provide members of many human gene families, we are investigating the TGD. An understanding of the mechanisms that guided evolution after the TGD requires comparisons to an appropriate outgroup -- an experimentally tractable species representing the most recently diverging lineage before the TGD. We exploited massively parallel DNA sequencing to develop strategies and software to construct, with thrift and speed, a meiotic map containing over 8,000 single nucleotide polymorphisms (SNPs in RAD-tags), including nearly a thousand protein-coding markers. Using a pseudotest cross strategy, we constructed a female map from a single individual wild-caught spotted gar female and made a male map from her mate. An RNA-seq project associated RAD-tags to protein-coding sequences. Results showed that the spotted gar genome diverged from the teleost genome before the TGD and resembles more closely the organization of the human genome than that of the teleost genome. We conclude that the spotted gar provides a critical link between teleost medical models, to which gar is biologically similar, and humans, to which gar is genomically similar. The comparison of sequenced gar genomic clones to teleost duplicated genes revealed the partitioning of conserved non-coding elements (CNEs) between teleost gene duplicates, and that these gar sequences can drive appropriate expression of a reporter in zebrafish embryos. Application of our mapping strategy and software promises to facilitate comparative genomic analysis in non-model species and help us to understand the principles by which genes likely evolved after the vertebrate genome duplication to shape the evolution of the human genome.
Contact : John POSTLETHWAIT