Evolutionary genomics is the study of the history of the genome. The focus of the evolutionary genomics group lies in the analysis of genomic data with respect to evolutionary aspects. Today we have many completed genomes available, which gives us the opportunity to elucidate the evolutionary processes that acted upon these genomes. Research in our group focuses in the use of comparative genomics to learn about the evolution and function of genes and genomes. We search for the footprints of natural selection and evolutionary innovation, and analyze the patterns of variation of substitution rates across different genes and time periods. Very important part of our research represent transposable elements that are the single largest component of the eukaryotic genomes and represent a major force driving evolution of organisms. They have contributed both directly and indirectly to the evolution of genome structure and function. The recent availability of large quantities of genomic sequence has led to a shift from the genetic characterization of single elements to genome-wide analysis of enormous transposable-element populations. We wants to understand the origin of transposable elements, how they are lost and gained by a species and the role they play in the processes of genome evolution.
We employ diverse methods of molecular, genomic, evolutionary and computational biology to perform research in numerous directions:
-PLA2 neurotoxins (2, 3, 4, 6, 8, 12),
-BPTI neurotoxins (11),
-molecular evolution of protease inhibitors (13, 18),
-adaptive evolution of neurotoxins (3, 6, 8, 12, 13),
-functional diversification after gene duplication (8, 11, 12, 18),
-evolution of multidomain proteins (18),
-phylogenomic analysis of protein superfamilies (15, 18),
-phylogenomic analysis of retroelements (10, 11, 14, 16, 17, 19),
-origin and the evolution of the single largest genome component of eukaryotes: Chromoviruses (14, 16, 17),
-origin and evolution of the largest genome component of the mammals: L1 retroposons (19),
-evolutionary dynamics of diverse retroelements (5, 7, 9, 10, 11, 14, 16, 17, 19),
-horizontal gene transfer (1, 3, 5, 7, 9, 11, 14, 15, 16, 17),
-comparative and evolutionary genomics of protein superfamilies and retroelements (10, 11, 14, 16, 17, 18, 19),
-genomic analysis of reptilian genomes (protein-coding genes and transposable elements) (1 – 14, 16, 17, 19),
-genomic analysis of metazoan and deuterostome genomes (protein-coding genes and transposable elements) (1 – 14, 16 - 19),
-gene and genome evolution in eukaryotes (5, 10, 11, 14, 16, 17, 18, 19),
-inhibition of HIV and MMTV replication (20-22).
1. Kordis, D. & Gubensek, F. (1995) Horizontal SINE transfer between vertebrate classes. Nature Genetics 10:131-132.
2. Kordis, D. & Gubensek, F. (1996) Ammodytoxin C gene helps to elucidate the irregular structure of Crotalinae group II phospholipase A2 genes. Eur. J. Biochem. 240:83-90.
3. Kordis, D. & Gubensek, F. (1997) Bov-B long interspered repeated DNA (LINE) sequences are present in Vipera ammodytes phospholipase A2 genes and in genomes of Viperidae snakes. Eur. J. Biochem. 246:772-779.
4. Gubensek, F. & Kordis, D. (1997) Venom phospholipase A2 genes and their molecular evolution. in: Kini, R.M. (ed.). Venom phospholipase A2 enzymes: structure, function and mechanism. Wiley, pp. 73-95.
5. Kordis, D. & Gubensek, F. (1998). Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc. Natl. Acad. Sci. USA 95:10704-10709.
6. Kordis, D., Bdolah, A. & Gubensek, F. (1998) Positive Darwinian selection in Vipera palaestinae phospholipase A2 genes is unexpectedly limited to the third exon. Biochem. Biophys. Res. Commun. 251:613-619.
7. Kordis, D. & Gubensek, F. (1999) Molecular evolution of Bov-B LINEs in vertebrates. Gene 238:171-178.
8. Kordis, D. & Gubensek, F. (2000) Adaptive evolution of animal toxin multigene families. Gene 261:43-52.
9. Kordis, D. & Gubensek, F. (2000) Horizontal transfer of non-LTR retrotransposons in vertebrates. in: MacDonald, J.F. (ed.). Transposable elements and genome evolution, (Georgia genetics review, vol. 1). Kluwer, pp. 121-128.
10. Lovsin, N., Gubensek, F. & Kordis, D. (2001). Evolutionary dynamics in a novel L2 clade of non-LTR reprotransposons in Deuterostomia. Mol. Biol. Evol. 18:2213-2224.
11. Zupunski, V., Gubensek, F. & Kordis, D. (2001) Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol. Biol. Evol. 18:1849-1863.
12. Kordis, D., Krizaj, I. & Gubensek, F. (2002) Functional diversification of animal toxins by adaptive evolution. in: Menez, A. (ed.). Perspectives in molecular toxinology. Wiley, pp. 401-419.
13. Zupunski, V., Kordis, D. & Gubensek, F. (2003) Adaptive evolution in the snake venom Kunitz/BPTI protein family. FEBS Lett. 547:131-136.
14. Gorinsek, B., Gubensek, F. & Kordis, D. (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol. Biol. Evol. 21:781-798.
15. Rezen, T., Debeljak, N., Kordis, D. & Rozman, D. (2004) New aspects on lanosterol 14-demethylase and cytochrome P450 evolution: lanosterol/cycloartenol diversification and lateral transfer. J. Mol. Evol. 59:51-58.
16. Kordis, D. (2005). A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 347:161-173.
17. Gorinsek, B., Gubensek, F. & Kordis, D. (2005) Phylogenomic analysis of chromoviruses. Cytogenet. Genome Res. 110:543-552.
18. Novinec, M., Kordis, D., Turk, V. & Lenarcic, B. (2006) Diversity and evolution of the thyroglobulin type-1 domain superfamily. Mol. Biol. Evol. 23:744-755.
19. Kordis, D., Lovsin, N. & Gubensek, F. (2006) Phylogenomic analysis of the L1 retrotransposons in Deuterostomia. Syst. Biol. 55:886-901.
20. Zheng, Y.H., Lovsin, N. & Peterlin, B.M. (2005) Newly identified host factors modulate HIV replication. Immunol. Lett. 97:225-234.
21. Okeoma, C.M., Lovsin, N., Peterlin, B.M. & Ross, S.R. (2007) APOBEC3 inhibits mouse mammary tumour virus replication in vivo. Nature 445:927-930.
22. Aguiar, R.S., Lovsin, N., Tanuri, A. & Peterlin, B.M. (2008) Vpr.A3A chimera inhibits HIV replication. J. Biol. Chem. 283:2518-2525.
Members of the evolutionary genomics group: