Biology Reference
In-Depth Information
the basis of phenotypic (morphological) features or organismal biology, (iii) can the sequence-based
phylogenies provide answers and proofs of the reality of macroevolution? and (iv) how far LGT
(also designated as horizontal gene transfer by some workers) affects the tree-building?
LGT is found more frequently in prokaryotes than in eukaryotes. LGT occurs in prokaryotes by
means of transformation, conjugation and transduction. Genomic and phylogenetic analyses have
established beyond doubt the ubiquitous occurrence of LGT among prokaryotes. Among very close
relatives, homologous recombination is a great force to cause sequence divergence in many bacteria.
Homologous recombination is so widespread among the strains of a designated species that even the
housekeeping genes are not even spared. LGT events, on the other hand, occur across domains as for
example, from Archaea to Bacteria and from Bacteria to nuclear genomes of eukaryotes. Sequencing of
complete genomes and their analysis has contributed to a better understanding of LGT. On the basis
of genome comparisons of bacteria and archaea, it is possible to demonstrate that major fractions of
genes have been acquired through LGT events in many prokaryotes. It is signifi cant to note that in
a number of pathogenic bacteria (pathogenicity islands) and symbiotic bacteria (symbiosis islands)
over 30% of the genomes are acquired through events of LGT (Hacker and Kaper, 2000; Ochman
and Moran, 2001; Perna
et al
., 2001). There are very few orthologous gene sets whose history is free
of LGT (Gogarten
et al
., 2002; Gogarten and Townsend, 2005). Even genes such as those of ribosomal
proteins and RNA polymerases have not been spared (Brochier
et al
., 2000; Makarova
et al
., 2001;
Iyer
et al
., 2004). Based on the sequencing of
Arabidopsis
, chloroplast and cyanobacterial genomes, it
was possible to identify thousands of genes of cyanobacterial endosymbiont (the chloroplast) into
the host (plant) genome through LGT (Martin
et al
., 2002). Another 'big bang' that occurred due to
LGT is the evolution of mitochondria in eukaryotes. Alpha-proteobacterial ancestor of mitochondria
probably invaded an archaebacterial host triggering the genesis of a eukaryotic cell that signalled
the formation of endomembrane system, cytoskeleton and the nucleus (Martin and Muller, 1998;
Martin and Koonin, 2006).
There are at least three approaches to determine LGT events. The fi rst one is to determine
the atypical sequence characteristics such as codon usage bias and G+C content. Because codon
usage and G+C are species-specifi c, it was possible to identify genes up to 18% in
E
.
coli
as laterally
transferred genes (Lawrence and Ochman, 1998). Recent studies of Sorek
et al
. (2007) are indicative of
the fact that genuine barriers for LGT in this model organism are quite low as it virtually accepted all
prokaryotic genes offered to it
in vitro
. Likewise, approximately 24% of genes in
Thermotoga maritima
have come through LGT events (Garcia-Vallvé
et al
., 2000). The second method to detect LGT is to
reconstruct a phylogeny of genes. By this approach, it is possible to compare phylogenetic trees
among individual genes within closely related species and recognize unusual origins of genes. The
third alternative is to detect the presence/absence of genes in closely related bacteria. Though it is
quite not possible to detect the number of insertion and deletion events due to gene rearrangements,
it is possible to know the total number of genes due to insertions/deletions. Hao and Golding (2004)
analysed 50 bacterial complete genomes from nine groups, mapped the number of gene insertions,
deletions and gene duplications onto the phylogeny of the species based on 16S rRNA phylogeny.
The results revealed that the number of gene insertions was much larger in the external branches of
the trees and they greatly outnumbered the occurrence of deletions. At the same time, the genome
sizes of these bacteria remained roughly constant suggesting that these insertions were specifi c to an
organism and were lost before related species could evolve. Beiko and Charlebois (2007) developed
a new software program known as EvolSimulator that can perform gene-, protein- and genome-
scale evolutionary processes that occur in prokaryotes. It can simultaneously create lineages, gene
families and sequence substitutions that can measure the levels of LGT events. Dagan
et al
. (2008)
