euGenes is a genome information system and database that provides a common summary of eukaryote genes and genomes, at http://iubio.bio.indiana.edu/eugenes/. Seven popular genomes are included: human, mouse, fruitfly, Caenorhabditis elegans worm, Saccharomyces yeast, Arabidopsis mustard weed and zebrafish, with more planned. This information, automatically extracted and updated from several sour...

Ligninolytic fungi are unique among eukaryotes in their ability to degrade polycyclic aromatic hydrocarbons (PAHs), but the mechanism for this process is unknown. Although certain PAHs are oxidized in vitro by the fungal lignin peroxidases (LiPs) that catalyze ligninolysis, it has never been shown that LiPs initiate PAH degradation in vivo. To address these problems, the metabolism of anthracen...

Determining the precise position of the root of the eukaryote evolutionary tree is very important for understanding cell evolution [1], but has been a major challenge, because of systematic biases in gene sequence trees [2,3]. However, one can deduce the position indirectly, by using derived genic properties to exclude the possibility that the root lies within clades that share them [4]. A deri...

Stearoyl-CoA desaturase (SCD) is a key enzyme that converts saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs) in the biosynthesis of fat. To date, two isoforms of scd gene (scd1 and scd5) have been found widely existent in most of the vertebrate animals. However, the evolutionary patterns of both isofoms and the function of scd5 are poorly understandable. Herein, we aim to cha...

This paper supports a previous conjecture that the sexual cycle of eukaryotes arose from the infection of cells by genome parasites. The finding are as follows. (1) In prokaryotes, conjugative plasmids ensure their own spread by directing partial cell fusion. (2) Conjugative plasmids permit gene transfer between prokaryotes and eukaryotes, and can be integrated into the eukaryote genome. (3) Ge...

Extrachromosomal DNA elements have been identified in wild-type populations of the parasitic protozoan Leishmania. Elements from L. major and L. tropica were detected using orthogonal-field-alternation-gel electrophoresis. They are nonhomologous, supercoiled circular DNA molecules derived from different chromosomes in the Leishmania genome. Electron microscopy revealed that the elements have ve...

If we took all of the single copy genes in all sequenced genomes, made phylogenetic trees from them individually, and then made the supertree of those trees, what would we get? Recently, David Pisani and colleagues did that experiment and their results are likely to spark much discussion. Their prokaryote tree looks very familiar, but the genome history of eukaryotes appears dominated by genes ...