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Evolution of gene clusters in amphibians: a phylogentic and genomic approach

Tuesday, 15 February, 2011 - 17:00
Campus: Brussels Humanities, Sciences & Engineering campus
Faculty: Science and Bio-engineering Sciences
An Mannaert
phd defence

In the vertebrate evolutionary tree, amphibians occupy an essential position as
ancient tetrapods. They form a transitional group between swimming fishes and
land-dwelling amniotes, and are therefore key representatives of the fin-to-limb
transition. In addition, amphibians exhibit many unique features, such as very
diverse body plans and limb types between frogs, salamanders and caecilians, or a
wide range of genome sizes between and within the three orders. This work deals
with the genomic aspects that may have contributed to these characteristics, by
studying the evolution of two clustered gene families that are likely to have played
a role in the diversification of amphibians. Both gene families, Hox genes and TIL
protein-encoding genes, have a different evolutionary history. Hox genes are
essential for body patterning in all animals (except sponges) and are therefore
highly conserved. TIL protein-encoding genes on the other hand exist only in
amphibians and are thought to play a role in host defense, either as toxin, or as
part of the innate immune system.

First, a PCR survey for Hox genes involved in limb development was conducted
in two species of the three amphibian orders, which confirmed the presence of
four clusters in all amphibians. Moreover, not every gene that was expected based
on the Hox complement of other vertebrates was recovered, suggesting that
lineage-specific losses occurred in amphibians. Next, a BAC library of a caecilian
was constructed in order to obtain the HoxD cluster for comparative analyses with
other vertebrates, including the identification of conserved, non-coding sequences
or putative regulatory elements. At least one regulatory element present in other
vertebrates was lost in amphibians. Strikingly, the caecilian posterior HoxD cluster
has experienced the loss of one gene and the accumulation of transposable
elements and other repeats, resulting in a considerable expansion of the cluster.
This may exert an influence on the long-range enhancer regulating the expression
of the posterior Hoxd genes during limb development, and may be correlated with
the elongation of the caecilian body and absence of limbs.

The TIL protein-encoding genes were identified in the skin of distantly related
frog species and in a salamander. These genes encode a protein domain that is
also found in serine protease inhibitors, venom and anticoagulant proteins of
(blood-feeding) arthropods and nematodes. In vertebrates, this domain is present
in large, structural, multi-domain proteins, but the TIL protein architecture only
exists in amphibians. All but a few amphibian TIL protein-encoding genes form a
single clade, together with trypsin inhibitors from Bombina frog species. This gene
family is characterized by extensive gene duplications and rapid diversification,
which may be related to their putative toxin or immune function. Each in a
different way, both gene families have contributed to the evolutionary
diversification of amphibians.