4 Jun
2013
4 Jun
'13
10:52 a.m.
Dear Barcelona Evo-Deviants,
Toni Gabaldon will be hosting Michel Milinkovitch next week at the CRG. His seminar will
be on reptilian phylogenomics and evo-devo (see below).
Best,
Yogi
--- seminar announcement: ----
Wednesday, June 12th, 15:00 h
Sala Charles Darwin (PRBB)
Reptilian-transcriptomes.org: from phylogenomics to EvoDevo.
Michel C. Milinkovitch
Laboratory of Artificial & Natural Evolution (LANE)
Dept of Genetics & Evolution, University of Geneva, Switzerland.
Reptiles are largely under-represented in comparative genomics/transcriptomics despite the
fact that they are substantially more diverse in many respects than mammals. We performed
deep-sequencing of transcriptomes of divergent reptilian and avian lineages and used
in-house software pipelines for recursive similarity searches and homology assignment. Our
approach identifies the majority of the reference chicken transcripts and about 50% of
de-novo assembled reptilian transcripts. We also identify dozens of thousands
microsatellite, SNP, and indel polymorphisms for population genetic and linkage analyses.
We build very large multiple alignments (hundreds of thousands residues per species) and
generate the first robust large-scale phylogenomic hypothesis for Sauropsida and mammals.
Our analyses indicate that turtles are not basal living reptiles but are rather associated
with Archosaurians, hence, answering a long-standing question in the phylogeny of
Amniotes.
We also deep-sequenced in snakes the transcriptome of the vomeronasal organ (VNO), an
olfactory structure that detects pheromones and environmental cues. Snakes exhibit a very
large VNO associated with a sophisticated tongue delivery system. The predominant V1R and
V2R transmembrane chemoreceptor repertoires in tetrapods are believed to detect airborne
and water-soluble molecules, respectively. It has been suggested that the shift in habitat
of early tetrapods from water to land is reflected by an increase in the ratio of V1R/V2R
genes. Our analyses indicate that snakes and lizards retain an extremely limited number of
V1R genes but exhibit a large number of V2R genes, including multiple lineages of
reptile-specific and snake-specific expansions. These results do not support the
hypothesis that the shift to a vomeronasal receptor repertoire dominated by V1Rs in
mammals reflects the evolutionary transition of early tetrapods from water to land.
Instead, our study reveals how mammals and squamates differentially adapted the same
ancestral vomeronasal repertoire to succeed in a terrestrial environment.
The reptilian transcriptomes (freely available at http://www.reptilian-transcriptomes.org)
should prove useful new resourcea as reptiles are becoming important new models for
comparative genomics, ecology, and evolutionary developmental genetics.