Hox and ParaHox in tunicates: genomic organization, regulation and biogeography

Caputi, Luigi (2007). Hox and ParaHox in tunicates: genomic organization, regulation and biogeography. PhD thesis The Open University.

DOI: https://doi.org/10.21954/ou.ro.0000fb2a


Hox and ParaHox were studied in the model invertebrate Ciona intestinalis (Urochordata) in respect of their role in evolution and development. The principal aims of this thesis work were to define genetic distances between Hox and ParaHox genes and to identify the positive regulatory region of the CiHox5 gene.

In order to resolve the genetic distances between those Hox and ParaHox genes that have maintained clustered topology within the Ciona genome, a classical genetic approach (backcross) was used. Genetic polymorphism of Hox and ParaHox markers was characterized at large and small geographical scales using one British and two Neapolitan populations. Classical genetics was supported by the modem Single Nucleotide Polymorphism technique. Physical distance in cM (Haldane’s function) was calculated to be 8.4 cM for the two genetic loci CiHox-5 and -70; linkage disequilibrium values D’ and r2 for the same loci were calculated to be, respectively, of 0.92 and 0.74.

A dataset obtained from the above analysis was used to establish the phylogenetic relationships between C. intestinalis strains, leading to the discovery of cryptic speciation within the genus. Two species, preliminarily named Ciona intestinalis spp. A and B, have been identified. The two species have, respectively, a Pacific- Mediterranean and a North Atlantic distribution and coexist in the English Channel. Hox and ParaHox data were complemented by COI phylogenetic analysis, sexual compatibility trials and morphological data. The different genetic behaviour of the two species was analysed.

The Hox5 gene was chosen as a case study for developmental analysis. In order to identify the promoter region of the gene and to uncover basic mechanisms of persisting spatial colinearity in organisms with unclustered Hox genomic topology, a transgenic approach was used. Preliminary transgenic results identify a 1 kb region, while in silico results restrict the analysis to two small regions.

Viewing alternatives

Download history


Public Attention

Altmetrics from Altmetric

Number of Citations

Citations from Dimensions

Item Actions