PHYLOGENETIC ANALYSIS AND HOMOLOGY MODELLING OF LACCASE GENE OF FUSARIUM OXYSPORUM Lcc2. * S.Arul Diana Christie 1 and S.Shanmugam 2 1 Research and Development Centre , Bharathiar University Coimbatore. 2 Department of Microbiology, Government Arts College (Men),Krishnagiri. E.Mail: dianajoels@gmail.com ABSTRACT Morphological identification of fungi is the first and the most difficult step in the identification process. This is especially true for Fusarium species. Fusarium has a cosmopolitan distribution. Fusarium sp was isolated from Anamalai Hills region and Subjected to Morphological identification using standard microbiological methods. Genotypic identification was carried out by PCR amplification and partial sequencing of the 16S rRNA for the confirmation of morphological identity. The rDNA sequence of 16S ribosomal RNA gene was amplified by PCR and the PCR product .The fungus, was bi directionally sequenced using forward and reverse primers. Using BLAST Tool the sequence was searched for the similarity matches .F.oxysporum shows maximum similarity. The Gene of the species was obtained from Uniprot. Since the unavailability of the 3D structure of Fusarium Laccase gene this attempt was carried out and Homology modeling was performed using Modeller Tool. Key Words: Homology Modelling, Laccase, Lcc2 gene, F.oxysporum. I.INTRODUCTION Morphological identification of fungi is the first and the most difficult step in the identification process. This is especially true for Fusarium species. Fusarium has a cosmopolitan distribution. Although morphological observations may not suffice for complete identification, a great deal of information is usually obtained on the culture at this stage. Morphological and biochemical distinctiveness of fungi are universally used for their identification, but differentiation of closely related cultures require extensive molecular techniques (Shahriarnour et al., 2011). Many researchers turn to molecular systematics as an alternative or a complementary tool to classical taxonomy. Central to this is the decision over which molecular marker to use, that will give the closest interpretation of the conventional morphological data. The internal transcribed spacer (ITS) regions of the ribosomal DNA (rDNA) has become a more popular marker for systematics and phylogenetic studies of closely related species of animals, plants and fungi (Von der Schulenburg et al., 2001). PCR amplification with universal primers targeted to conserved regions within the rRNA complex and subsequent DNA sequencing of the internal transcribed spacer (ITS) regions, shows promise to identify a broad range of fungi to the species level (Chen et al., 2001). The PCR primer sets routinely used for amplification of ITS regions and rDNA are known to be ITS1 and ITS4 (White et al., 2001) One of the most widely used methods for detecting homologous sequences is Blast. The Blast suite of programs is used to find local sequence similarities, which might lead to evolutionary clues about the structure and/or function of the query sequence. The detected sequences can then be used e.g. to build a multiple alignment of complete sequences (MACS), which represents an ideal workbench to study all the information related to a set of homologous sequences. (Anne Friedrich et al., 2007) To experimentally discover functionality of any protein, the information of its 3D structure remains an indispensable fact, which is achieved using techniques like X-Ray Crystallography or NMR spectroscopy. Experimental techniques are very tedious and prolonged and not always succeed in determining structure for all proteins especially membrane proteins (Johnson et al.1994). Moreover, the rate at which protein sequence data is accumulating is far more than the structural information available, thus creating a gap between available sequences and experimentally solved structures. Computational methods like homology modeling can help reduce this gap. It is known that existing proteins are result of continuous evolution of previously existing ones, thus proteins can be grouped into families Homology modeling methods use the fact that evolutionary related proteins share a similar structure. Therefore, models of a protein with unknown structure (target) can bebuilt based on an alignment of a protein of known structure (template). This typically involves four steps (Sánchez S.Arul Diana Christie et al. / International Journal of Pharma Sciences and Research (IJPSR) ISSN : 0975-9492 Vol 3 No 12 Dec 2012 571