ANalysis of multifunctiOnal genes and Their pAralogs in TEleosts: Identification, Evolution and Annotation through Transcriptome scans and Functional studies

Aim of the present proposal is to identify, characterise and annotate new or known duplicated genes across
teleost and non-teleost fish species, to search for their paralogs gene(s) and to examine the possibility of new
gene families (if more then one paralogs is found). Therefore a three level approach is suggested. The first
level investigates the identification of duplicated genes via transcriptome scans through main marine
teleost fish orders and subsequently performs first annotations using BLASTN and BLASTX search against
NCBI, Ensemble and other fish specific databases. Further annotation like pattern search, structural
characterization and domain detection will be performed. The second level comprises evolutionary studies
of the identified genes throughout the selected marine fish species including phylogenetic analysis, synteny
analysis, investigations to unravel whether genes under study or gene groups evolve at different rates, gene
loss and whether Darwinian selection has occurred. The third level concerns functional studies of the
candidate gene set. It is expected to detect diversifications between paralogs genes in terms of expression
and evolution. In addition extended research for selected genes will be carried out to determine possible
multifunctional properties. Multifunctional properties have been shown for genes which originally were
assigned to classical functions like for example Glyceraldehyd-3-phosphate (GAPDH) or warm temperature
acclimation protein 65 (WAP65). The former is known as classical housekeeping gene. However divers
studies have shown its implementation in development and immune response [1]. Concerning WAP65, it
was primarily identified due to increased expression associated with warm temperature acclimation of gold
fish and carp [2,3]. In contrast to heat-shock proteins, which were first identified after short-term adjustment,
Wap65 was found to be higher expressed due to temperature acclimation (Kikuchi et al., 1993). The term
“heat shock protein” was chosen based on early observations on Drosophila exposed to heat stress. Today
heat-shock proteins can be up-regulated in cells that are exposed to a broad range of stressors. Similar the
term “warm-temperature protein” was assigned to a 65-kDa protein due to its high abundance in various
tissues after warm temperate acclimation. At present several studies showed that Wap65 proteins are
involved in development, immune response as well as stress response. In the viewpoint of evolution it is of
interest to explore whether multifunctionality inhibits adaptability (e.g. by presence or absence of paralogs)
or whether organisms profit of multifunctional genes. The outcome of ANnOTATE will highly interest
researchers studying gene evolution as well as for researchers interested in candidate genes for biomarker
linked to the immune response, egg quality and environmental adaptation. In addition it will contribute
significantly to the appropriate annotation of fish genes taking into account the evolutionary relationships of
paralogs that have arisen in different vertebrate lineages. The enrichment of the dataset of hagfish as well as
for sturgeon is of importance not only to identity the homologues genes which will contribute to
phylogenetic analysis and will shed light into the original function of the transcripts but also to the hagfish
and sturgeon community. In long-term aspect the outcome may be of importance also in biomedical research
as belonging to the vertebrates, several research results in teleosts species have been served as groundwork
in human disease research.