Sequence analysis of an amphioxus cosmid containing a gene homologous to members of the aldo-keto reductase gene superfamily

Gene finding in novel genomes

Background

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.

Results

I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate.

Conclusion

Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

Were vertebrates octoploid?

It has long been suggested that gene and genome duplication play important roles in the evolution of organismal complexity. For example, work by Ohno proposed that two rounds of whole genome doubling (tetraploidy) occurred during the evolution of vertebrates: the extra genes permitting an increase in physiological and anatomical complexity. Several modifications of this 'two tetraploidies' hypothesis have been proposed, taking into account accumulating data, and there is wide acceptance of the basic scheme. In the past few years, however, several authors have raised doubts, citing lack of direct support or even evidence to the contrary. Here, we review the evidence for and against the occurrence of tetraploidies in early vertebrate evolution, and present a new compilation of molecular phylogenetic data for amphioxus. We argue that evidence in favour of tetraploidy, based primarily on genome and gene family analyses, is strong. Furthermore, we show that two observations used as evidence against genome duplication are in fact compatible with the hypothesis: but only if the genome doubling occurred by two closely spaced sequential rounds of autotetraploidy. We propose that early vertebrates passed through an autoautooctoploid phase in the evolution of their genomes.

Characterization of the amphioxus presenilin gene in a high gene-density genomic region illustrates duplication during the vertebrate lineage

Molecular studies on the pathology of Alzheimer's disease (AD) have revealed that mutations in presenilin genes (PS) account for some familial cases. Although the contribution of these genes to the etiology is clear, their biological function remains obscure. Approaches using model organisms have been hampered by the fact that rodents contain two PS copies in the genome and do not develop the hallmark features associated with AD upon aging. To understand PS function and evolution, we have searched for PS homologous sequences in the genome of a lower chordate, Branchiostoma floridae. We report the structure of a single copy Branchiostoma floridae PS gene, named BfPS, and describe new features at the molecular level. Moreover, molecular phylogenetic analysis suggests that BfPS is orthologous to the vertebrate PS-1 and PS-2 forms. Finally, the analysis of more than 16 kb of genomic DNA encompassing BfPS identified three novel genes, which cluster with BfPS in a high gene-density region.