Global extent of horizontal gene transfer Export

@article{citeulike:2643589, abstract = {10.1073/pnas.0611557104 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 (\^{a}‰ˆ8,000) listed in the Pfam database. The results suggest four conclusions: () 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\^{a}€“9.7\% of Pfam families surveyed at three taxonomic ranges studied show indication of HGT); () however, at the level of domains, >50\% of Archaea have one or more protein domains acquired by HGT, and nearly 30\^{a}€“50\% of Bacteria did the same when examined at three taxonomic ranges. But, the equivalent value for Eukarya is <10\%; () 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 () there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions.}, address = {Physical Biosciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, CA 94720, USA.}, author = {Choi, In-Geol and Kim, Sung-Hou}, citeulike-article-id = {2643589}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0611557104}, citeulike-linkout-1 = {http://www.pnas.org/content/104/11/4489.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/104/11/4489.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/17360551}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=17360551}, day = {13}, doi = {10.1073/pnas.0611557104}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {evolution, horizontal\_gene\_transfer, phylogenetic\_trees, tree\_of\_life}, month = {March}, number = {11}, pages = {4489--4494}, posted-at = {2009-11-04 11:27:56}, priority = {2}, title = {Global extent of horizontal gene transfer}, url = {http://dx.doi.org/10.1073/pnas.0611557104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:2643589 L3 - citeulike-article-id:2643589 N2 - 10.1073/pnas.0611557104 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 (≈8,000) listed in the Pfam database. The results suggest four conclusions: () 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); () 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%; () 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 () there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions. IS - 11 JF - Proceedings of the National Academy of Sciences SN - 0027-8424 AD - Physical Biosciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, CA 94720, USA. EP - 4494 TI - Global extent of horizontal gene transfer VL - 104 SP - 4489 KW - evolution KW - horizontal_gene_transfer KW - phylogenetic_trees KW - tree_of_life AU - Choi, In-Geol AU - Kim, Sung-Hou PY - 2007/03/13/ UR - http://dx.doi.org/10.1073/pnas.0611557104 ER -