PhD thesis

64 Submitted manuscript
Chapter IV
encode transcription factors which
activate gene cascades (Hueber and
Lohmann 2008). In the case of the
Not gene, which plays an important
role during notochord formation in
vertebrates (Stein and Kessel 1995,
Talbot et al. 1995, Gont et al. 1996, Stein
et al. 1996, Abdelkhalek et al. 2004),
the downstream genes are known to
regulate mesoderm formation in sea
urchins as well as left/right patterning,
notochord, mesoderm, and somite
formation in vertebrates (Peterson et
al. 1999, Yasuo and Lemaire 2001,
Beckers et al. 2007). Homologs of
the homeobox gene Not have been,
among others, identified in Xenopus
(Xnot), chick (Gnot1, Gnot2), zebrafish
(flh), mouse (noto), Hydra (HvuNot),
Drosophila (90Bre), and the basal
eumetazoan Trichoplax adhaerens
(TadNot), but the developmental
role of Not in invertebrates without a
notochord is largely unknown (Dessain
and McGinnis 1993, von Dassow et al.
1993, Knezevic et al. 1995, Odenthal
et al. 1996, Gauchat et al. 2000,
Martinelli and Spring 2004, Hoskins
et al. 2007). A Not homolog seems
to be lacking in the model sponge
Amphimedon queenslandica (Bernard
Degnan, personal communication).
However, the presence of a Not gene
in cnidarians and Trichoplax indicates
that it was present prior to the evolution
of the mesoderm, and thus long
before the evolution of the notochord.
Accordingly, the ancestral role of Not
remains elusive. Given its confirmed
absence in the poriferan genome
would make it a good candidate for a
eumetazoan apomorphy.
Cdx is a member of the ParaHox gene
cluster which probably originated by
duplication from an ancestral ProtoHox
gene cluster which led to the Hox and
ParaHox clusters, respectively (Brooke
et al. 1998). Cdx has been found to be
involved in the development of posterior
tissues of almost all animal phyla in
which it has been investigated and is
thus often termed “caudal” (Epstein et
al. 1997, Copf et al. 2004). In addition
to the posterior tissues, it was found
to be expressed in the mesoderm of
taxa as diverse as Artemia, Capitella,
Patella, Branchiostoma, and Mus;
in the gut of Drosophila, Capitella,
Branchiostoma, and Mus; and in the
central nervous system of Capitella,
Branchiostoma, and Mus (Macdonald
and Struhl 1986, Duprey et al. 1988,
Le Gouar et al. 2003, Copf et al.
2004, Fröbius and Seaver 2006). Cdx
is absent in the recently sequenced
poriferan Amphimedon queenslandica
(Larroux et al. 2008, Srivastava et
al. 2010), but a gene related to Cdx
is present in Nematostella vectensis,
a representative of Cnidaria, the
proposed sister group to Bilateria
(Chourrout et al. 2006, Quiquand et
al. 2009).
The phylogenetic position of
Brachiopoda within Bilateria is still
controversial (Williams and Carlson
2007, Hejnol et al. 2009, Paps et al.
2009). Most authors include them within
Lophotrochozoa, but their position
within this clade remains unresolved,
and some authors consider them a
sister group to Deuterostomia (Nielsen
2002). Within the phylum, Brachiopoda
comprises three clades: Linguliformea,
Craniiformea, and Rhynchonelliformea.
Linguliformea and Craniiformea are
often considered sister groups and
were traditionally termed “inarticulate”,