Global extent of horizontal gene transfer

Abstract

Horizontal gene transfer (HGT) is thought to play an important role in the evolution of species and innovation of genomes. There have been many convincing evidences for HGT for specific genes or gene families, but there has been no estimate of the global extent of HGT. Here, we present a method of identifying HGT events within a given protein family and estimate the global extent of HGT in all curated protein domain families (Ϸ8,000) listed in the Pfam database. The results suggest four conclusions: (i) for all protein domain families in Pfam, the fixation of genes horizontally transferred is not a rampant phenomenon between organisms with substantial phylogenetic separations (1.1-9.7% of Pfam families surveyed at three taxonomic ranges studied show indication of HGT); (ii) however, at the level of domains, >50% of Archaea have one or more protein domains acquired by HGT, and nearly 30 -50% of Bacteria did the same when examined at three taxonomic ranges. But, the equivalent value for Eukarya is <10%; (iii) HGT will have very little impact in the construction of organism phylogeny, when the construction methods use whole genomes, large numbers of common genes, or SSU rRNAs; and (iv) there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions.protein domain family ͉ protein sequence family ͉ lateral gene transfer O ne of the new important concepts that emerged from a large number of genomic sequences in the last decade is that of horizontal gene transfer (HGT): gene transfer among organisms of different species. HGT has been found to have occurred in all three domains: Archaea, Bacteria, and Eukarya. The concept of HGT has been evoked to interpret various evolutionary processes ranging from speciation and the adaptation of organisms to uncertainties in phylogenetic inference of the tree of life (1-9). Although HGT has been regarded as a driving force in the innovation and evolution of genomes, especially in prokaryotes, its extent and impact on the evolutionary process and phylogeny of organisms or species remains controversial (8-10).There have been several methods developed to detect HGT, including (i) difference between gene trees derived from a limited number of gene families and the reference trees such as the small-subunit ribosomal RNA (SSU rRNA) tree (11-13) or whole genome tree (14); (ii) unexpectedly high sequence similarity of a gene from two distant genomes compared with those among homologous genes in closely related genomes (15); and (iii) unusual nucleotide composition or codon usages of a gene compared with the rest of the genes within a genome (16,17). Many factors affect the detection of HGT, such as lineage-specific gene loss (18,19), unequal rates of base substitution (1), loss of signal due to amelioration processes (16), and others (1, 15).It has been suggested that HGT may have been ''rampant'' in primitive genomes (6,20), but, for modern organisms, it may not be a dominant factor in speciation, because HGT has less effect on overall ge...

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

“…Our results show that the functional distribution of transferred genes is not random, as suggested earlier (Choi and Kim 2007). The abundance of metabolic genes and scarceness of informational genes within the dLGT network are in agreement with the complexity hypothesis (Jain et al 1999), according to which informational genes are transferred less frequently than those in the operational class.…”

Predicting microbial traits with phylogenies

“…The weaker phylogenetic signals detected in prokaryotes compared with eukaryotes can also arise from the horizontal transfer of genes, which is a remarkable natural source of variation (Dagan et al, 2008). This might weaken the signal by partly shuffling the traits in the phylogeny but does not blur it as the fixation of horizontally transferred genes is not substantial between phylogenetically distant microbes (Choi and Kim, 2007). Other numerous evolutionary processes show complex relationships with the phylogenetic signal of traits as has been thoroughly discussed (Revell et al, 2008).…”

Horizontal gene transfer in evolution: facts and challenges

“…Despite these caveats, a lot of work has been carried out in the last few years to try to deal with the importance of horizontal gene transfer in Bacteria and Archaea evolution (Faguy & Doolittle 1999;Nelson et al 1999;Ochman et al 2000;Ochman 2001;Gogarten et al 2002;Kurland et al 2003;Philippe & Douady 2003;Pál et al 2005a;Choi & Kim 2007;Koonin & Wolf 2008), and the attained results are controversial depending on whether the emphasis is placed on gene transfer or gene loss (Kurland et al 2003). However, the emergent picture is that horizontal gene transfer plays a larger role in microbial evolution than previously thought.…”