Giuseppe D'Onofrio
Giuseppe D'Onofrio
affiliation: Stazione Zoologica Napoli
research area(s): Computational Biology
Course: Computational Biology and Bioinformatics
University/Istitution: Università di Napoli Federico II
1979: M.D. (cum laude), University of Naples, Italy. Thesis on: The role of nucleic acids in rat brain during deprivation of paradoxical sleep. Director of the laboratory: Prof. A. Giuditta.
1981: Guest research associate at the Neurobiology Institute of Göteborg (Sweden), in the laboratory of Prof. H. Hydén.
1983-88: Research fellow at the Stazione Zoologica A. Dohrn of Naples (SZN), Dept. of the Laboratory of Dr. A. D'Aniello and Prof. J.M. Denucè (Nijmegen, Holland).
1989: Permanent researcher at the SZN
1989-93/ 98: Research fellow at the Institute J. Monod , University of Paris VII, Paris (France) in the Laboratory of Prof. G. Bernardi.
1994-97: Researcher at the SZN in the laboratory of Marine Biology of Dr D. Marino.
1999: First researcher at the SZN. Lab. of Molecular Evolution directed by Prof. G. Bernardi.
2009-11: PI in the group Animal Physiology and Evolution (APE) of SZN.

1989 Instructor for the Training course on "Biotin labeling in the detection of DNA" University of Harare (Zimbabwe)/ (UNESCO)
1996 – 2007 Member of the PhD Committee SZN (OPEN University) - Naples -Italy
2003 Director of Bioinformatics course (ICRO - UNESCO) Naples -Italy
2004 – 2007 Officer of the International Union of Biological Science (IUBS)
2008- Member of “Collegio dei Docenti”, Bioinformatic course –Univ. Federico II (Naples - Italy)
2012 Organizer of the EMBO course on Bioinformatics - Naples 11-17 May
In the last years,I focused on two main lines of research:
a) The nature of the forces driving the GC content variability among genomes;
b) The evolution rate of tunicates.
Regarding the first point, several hypotheses have been proposed to explain the genome base composition (GC content, i.e. the molar ratio of guanine plus cytosine): the mutational bias (MB), the biased gene conversion (BGC), the thermal stability (TS) and the metabolic rate (MR). Recently, an comprehensive analysis of teleostean fish (Uliano et al., 2010) strongly supported the MR hypothesis. Indeed, grouping teleostean fish in five broad habitats (polar, temperate, sub-tropical, tropical and deep-water), the MR of polar fish turned out to be the highest. Temperate fish displayed a significantly higher MR than sub-tropical and tropical fish, which had the lowest average value. The apparent agreement with the cold adaptation hypothesis was contradicted by the fact that the MR of fish living in deep-water was not significantly different from that of tropical fish, stressing that the oxygen dissolved in the water directly affects MR adaptation. The genomic GC levels showed a decreasing trend similar to that of MR. Plotting the genomic GC levels versus the MR a significant positive correlation was found. A detailed analysis of genomic doublets (namely CpG, TpG and CpA) in all fish genomes completely sequenced, discarded definitively a possible methylation/deamination effect (Chaurasia et al., 2011; in press)
Regarding the second point, in spite of the great attention devoted to the genome of tunicates, no data were available about the evolution rate of the “vertebrate’s sister group”. Combining data on coding sequences of Ciona intestinalis and Ciona savignyi with vertebrate fossil records: i) we estimated the time of divergence between the two ascidians nearly 180My; and that ii) on average Ciona species evolve 50% faster than vertebrates (Bernà et al., 2009).
Even trickier is the case of O. dioica. Indeed, this organism is showing an amino acid evolution rate never observed before for an eukaryotic organisms, raising the puzzle of the protein structure conservation due to an amazing low level preservation of the Cys residues (Bernà et al., 2011, submitted).

L. Bernà, G. D'Onofrio F. Alvarez-Valin, (2011). Peculiar patterns of amino acid substitution and conservation in the fast evolving tunicate Oikopleura dioica.
Mol. Phylogenet. Evol. - submitted)
A. Chaurasia, E. Uliano, L. Bernà, C. Agnisola, G. D'Onofrio (2011). Does Habitat Affect the Genomic GC Content? A Lesson from Teleostean Fish: A Mini Review.
In: Fish Ecology. Nova Science Publishers, Inc. Hauppauge NY (USA). In press
E. Uliano, A. Chaurasia, L. Bernà, C. Agnisola, G. D'Onofrio (2010). Metabolic rate and genomic GC. What we can learn from teleostean fish. Marine Genomics 3:29-34
L. Bernà, F. Alvarez-Valin, G. D'Onofrio (2009) How fast is the sessile ciona?
Comp Funct Genomics. doi: 10.1155/2009/875901
G. D'Onofrio, Ghosh, T. C., Saccone S. (2007) Different functional classes of genes are characterized by different compositional properties. FEBS Letters 581: 5819-5824
G. D'Onofrio, Ghosh, T. C. (2005). The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes.
Gene 345:27-33
Arhondakis, S., Auletta, F., Torelli, G., D'Onofrio G. (2004). Base composition and expression level of human genes. Gene 325, 165-169
G. D'Onofrio, (2002). Expression patterns and gene distribution in the human genome.
Gene 300, 155-160.
No projects are available to students for the current accademic year.