The European ribosomal RNA database

Wuyts, J.; Perrière, Guy; Peer, Yves Van de

doi:10.1093/nar/gkh065

Cited by 244 publications

(205 citation statements)

References 14 publications

Supporting

Mentioning

200

Contrasting

Unclassified

Order By: Relevance

“…(SI Tables 2 and 3). Of these, the gene sequences of SSU rRNA (16S rRNA of prokaryotes or 18S rRNA of eukaryotes) of 345 taxa were available from the European ribosomal RNA database (34). Among the SSU rRNA sequences belonging to each of 345 taxa, we chose the longest SSU rRNA sequence (but not Ͻ1,200 bases) to represent each taxon.…”

Section: Methodsmentioning

confidence: 99%

Global extent of horizontal gene transfer

Choi

Kim

2007

Proc. Natl. Acad. Sci. U.S.A.

121

View full text Add to dashboard Cite

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...

show abstract

Section: Methodsmentioning

confidence: 99%

Global extent of horizontal gene transfer

Choi

Kim

2007

Proc. Natl. Acad. Sci. U.S.A.

121

View full text Add to dashboard Cite

show abstract

“…Previously published sequences were retrieved from the rRNA database (Wuyts et al, 2004; http://www.psb.ugent.be/rRNA) for construction of the complete matrix. The employed in this analysis matrix uses a special distribution format, similar to the sequence files from the rRNA WWW server, to represent knowledge of secondary structure and to be identified by the alignment editor software Seaview (Galtier, 1996).…”

Section: Sequence Alignment and Partition Identificationmentioning

confidence: 99%

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

Wang

Kong

et al. 2008

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

“…Alignments of the 16S rRNA were subsequently carefully adjusted manually on the basis of 16S rRNA secondary structure of Ictalurus punctatus (GenBank accession No. AF032380) deposited in rRNA database (Wuyts et al, 2004). Gaps were considered as missing data rather than as fifth characters, to prevent those longer than one or two bases from being Hydrobiologia (2007) 579:55-68 57 taken as representing multiple events (Swofford, 1993).…”

Section: Sequence Alignment and Analysesmentioning

confidence: 99%

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Guo

Zhang

2007

Hydrobiologia

View full text Add to dashboard Cite

Several recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution.

show abstract

The European ribosomal RNA database

Cited by 244 publications

References 14 publications

Global extent of horizontal gene transfer

Global extent of horizontal gene transfer

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Contact Info

Product

Resources

About