Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning

We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones, Ail sequences have been minimally edited and searched against prot ein and DNA databases, These data are all displayed on a searchable, public ly available web site at http://fugu.hgmp.mrc,ac,uk/. With an average of 50 reads per cosmid, this is virtually nonredundant sequence skimming, coveri ng 30%-50% of each clone. This essentially random data set covers nearly 25 Mb (>6%) of the Fugu genome and Forms the basis of a series of whole genom e analyses which address questions regarding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalian genes. The Fugu genome, with eight rimes less DNA but a similar gene repertoire, is i deally suited to this type of study because most cosmids contain more than one identifiable gene. General features of the genome are also discussed. W e have made some estimation of the syntenic relationship between mammals an d Fugu and looked at the efficacy of ORF prediction From short, unedited Fu gu genomic sequences. Comparative DNA sequence analyses are an essential to ol in the functional interpretation of complex vertebrate genomes, This pro ject highlights the utility of using the Fugu genome in this kind of study.