galaxieEST: addressing EST identity through automated phylogenetic analysis

BACKGROUND: Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. RESULTS: galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download / local installation for use with any organism group at . CONCLUSIONS: By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and additional information on the query EST is needed

Phylogeny of Artiodactyla and Cetacea - based on mitochondrial genomes

Artiodactyla (eved-toed ungulates) and Cetacea (whales) are two mammalian orders that are commonly recognised as sistergroups. Recently it has been suggested that Cetacea originated within Artiodactyla, but the relationships among the different artiodactyl lineages and Cetacea have not been conclusively established. In the present study the mitochondrial genome of the pig (Sus scrofa), the hippopotamus (Hippopotamus amphibius), the alpaca (Lama pacos) and the sperm whale (Physeter macrocephalus) have been analysed. These sequences have been used in phylogenetic analyses together with those of two baleen whales, two ruminants and several other eutherian mammals. The study is based on the concatenated nucleotide and amino acid sequences (10,554 and 3,518 characters respectively) of all the mitochondrial protein coding genes except NADH6. Analyses on both data sets identified a basal divergence of the recent artiodactyls into Ruminantia (bovids, deers, tragulids and giraffs), Tylopoda (camels and llamas) and Suina (pigs and peccaries). However, the order in which these lineages diverged was not conclusively resolved. A clade of Ruminatia, Hippopotamidae (hippopotamuses) and Cetacea was identified where the sistergroup relationship between Cetacea and Hippopotamidae was well supported, making both Artiodactyla and Suiformes (pigs, peccaries and hippopotamuses) paraphyletic. Molecular data in conjunction with the palaeontological record have suggested that the primary divergence between recent whales into Odontoceti (toothed whales) and Mysticeti (baleen whales) occured 32-34 million years before present (MYBP). This calibration point suggests that the primary split between Ruminantia, Tylopoda and Suina occured at =65 MYBP, the divergence between Ruminantia and Hippopotamidae/Cetacea at 60 MYBP and the divergence between Hippopotamidae and Cetacea at =55 MYBP

Phylogeny of nematode-trapping fungi based on 18S rDNA sequences

The small subunit (SSU) ribosomal DNA (18S rDNA) from 15 species of nematode-trapping fungi and closely related non-parasitic species were sequenced. Phylogenetic analysis indicated that species within the genera of Arthrobotrys, Dactylaria, Dactylella, Monacrosporium and Duddingtonia formed a monophyletic and isolated clade among an unresolved cluster of apothecial ascomycetes. The phylogenetic patterns within this clade were not concordant with the morphology of the conidia nor the conidiophores, but rather with that of the infection structures. The results from the different methods of tree reconstruction supported three lineages; the species having constricting rings, the non-parasitic species and the species having various adhesive structures (nets, hyphae, knobs and non-constricting rings) to infect nematodes