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Online Journal of Bioinformatics
Volume 11 (1): 59-71, 2010.
In silico identification of functions enduring horizontal gene transfer in archaea.
Tamanna A1*, Nandi T1
1 Department of Biotechnology, Jaypee Institute of Information Technology University, Noida (UP) 201307, India.
Tamanna A1*, Nandi T., In silico identification of functions enduring horizontal gene transfer in archaea: a comparative approach. Onl J Bioinform., 11 (1): 59-71, 2010. A major route of genomic evolution in bacteria is the acquisition of new genes from often very distantly related individuals through horizontal gene transfer (HGT). Archaea sustaining extremophilic life, evolve by undergoing HGT to adapt to extreme conditions. With the availability of increasing amounts of genomic sequences, it is becoming evident that genomes experience horizontal transfer and integrate genetic information. However, the knowledge on the type of biological functions that is associated with such HGT remains scarce. Genome scale investigation of this issue will advance the understanding of functional classes of the genes that are involved in HGT. In this study, we have applied a comparative genomics approach to analyze 16 archaeal genomes that have been completely sequenced and assigned each gene with a HGT score according to w8 algorithm proposed by Tsirigos et al., 2005. We observed that the average fraction of proteins per proteome with ≥ 90% HGT score is 6.7%. The average fraction of proteins with significant sequence and function homology is 73.5% and 26.5%, respectively. Based on the comparative analysis at the sequence and function level, we have short-listed 54 unique protein functions that are more likely to undergo the phenomenon of HGT across 16 archaea. Cluster of Orthologous Groups (COGs) classification of the identified 54 protein functions revealed that the classes for energy production & conversion (C) and amino acid transporter & metabolism (E) are predominant. We have investigated the association of the biological function of genes and their preferences towards the phenomenon of horizontal gene transfer. This methodology can also be applied to the identification of biological functions associated with HGT in bacterial domain.
Keywords: Horizontal gene transfer (HGT).