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Analysis of Hox Genes in Ray and Lobed Finned Fish

Ed DiNunzio

            Evolutionary and Developmental Biology is a subsection of biology that studies the evolutionary and developmental relationships between organisms.  Advances in the fields of Genetics and Molecular Biology have allowed great strides to be made in Evo-Devo, although this is generally limited to studying organisms currently alive, or with fairly well preserved remains.  Among the genes focused on by Evolutionary Biologists, Hox genes are considered to be a paradigm and are the focus of great study.

             Hox genes are involved in the development of limb structures during embryogenesis.  Hox genes are organized into clusters containing up to 13 individual Hox genes. Thus far, no species has been found to contain all 13 possible Hox genes on a given Hox cluster. This is believed to be due to the fact that the number of genes in each cluster will differ among species due to duplication, mutations, or loss of gene events.  Additionally, the number of Hox clusters can vary from species to species, although this usually happens only among vertebrate species, studies of invertebrate species have thus far only one Hox cluster among invertebrates.

      Although invertebrate species only possess one Hox cluster, vertebrate species have undergone many duplications of their Hox clusters.  To date, no vertebrate species as been found to have less than 4 Hox clusters and several species have been found to have additional Hox clusters.  These Hox cluster duplications are believed to be important event in species evolution and divergence from existing species and are closely studied

The organization of Hox genes on a given Hox cluster plays an important role in the expression of each Hox gene.  Hox genes are expressed in a spatially collinear fashion, the order of the Hox gene from 5’ to 3’ determine if the gene is expressed in the anterior end or posterior end of the embryo. (3’ = anterior, 5’ =  posterior)  Additionally, Vertebrate Hox clusters also have a Temporal colinearity to their expression, gene expression progresses from one end of the cluster to the other end.  Invertebrate Hox clusters tend to lack this temporal colinearity, in part because of their short embryogenesis.

            While Hox genes are found in all vertebrate species, much research has been focused on the analysis of Hox genes in the Teleost fishes.  Teleost fish are ideally suited for Hox gene studies because they are the most diverse group of vertebrates, with over 25,000 species, and have several species which are already known to have undergone Hox cluster duplication.  In the Chiu lab, we are focused on the discovery and analysis of Hox genes and Hox clusters among the Zebrafish (Danio rerio), Bichir (Polypterus senegalus). and Pufferfish (Takifugu rubripes). 

Work in the Chiu-Lab has focused primarily on studying the Hox genes in a number of Teleost fish, including the Zebrafish (Danio rerio), Bichir (Polypterus senegalus), and Pufferfish (Takifugu rubripes).  This work focused primarily on the Hox-A cluster and the changes in both the coding regions and introns of these genes.  Sequence data from these Hox genes was analyzed in an attempt to clarify the rate of changes in these genes, as well as any patterns that these changes occur in.  Sequence data was also used to map phylogenetic relationships among the Teleost fish and to reinforce already existing phylogentic maps. Current work in the Chiu-Lab continues to focus on the study of Hox clusters in Teleost fish.  In an expansion of previous experiments, work is being performed on the Hox B and C clusters in the Bichir.  This work utilizes similar methods to that of previous work with the Hox A cluster.

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