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OJBTM
Online Journal of Bioinformatics
Volume
11 (1): 59-71, 2010.
In silico identification of
functions enduring horizontal gene
transfer in archaea: a comparative approach
Tamanna A1*, Nandi T1
1 Department of
Biotechnology, Jaypee Institute of
Information
Technology University, Noida (UP) 201307,
India.
ABSTRACT
Tamanna A1*, Nandi T., In
silico identification of functions enduring
horizontal gene
transfer in archaea: a comparative
approach. Online J
Bioinformatics 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).