Microsatellites characterization in the pink shrimp Farfantepenaeus notialis

Abstract

Currently more than 100 genome projects produce a flood of newly determined DNA sequences. To make this data useful it has to be converted into biological meaningful knowledge. This process, which is called annotation, is done in two steps. The first one is called gene finding. As a result the open reading frame of the genes are predicted. The translated amino acid sequences are required for the second step, where the functional and other biological information of the gene-product is determined. The result of the first step of annotation is crucial for the second one. Therefore, to pursue the second step of annotation carefully, an estimate is required, which sequences can be considered to be correctly predicted. The open reading frames can be assumed to be more reliable, if cDNA or similar protein sequences can be found that match to the predicted genes. Here we investigated which and how much of the sequences of the nematode C. elegans are confirmed by cDNA and related protein sequences. No cDNA hits could be found for 40% of the sequences, only 12% of the sequences are strongly confirmed by cDNA data. BLAST hits to protein sequences were found for about 80 % of the sequences. This data allows to estimate the reliability of the predicted genes, when working on the second step of the C. elegans annotation. for C. elegans Farfantepenaeus notiah 558 One Hypothetical Multisubunit membrane-bound piFe1Hydrogenase in Desulfovibrio gigas ITQB, Ap. 127, 2781-903, Oeiras-PortugalDesulfovibrio species are sulfate reducing bacteria rich in metalloproteins, which act as redox enzymes and electron carriers. Altough several studies have been made on the characterization of these proteins, the function of many of them remains poorly understood. Desulfovibrio gigas is a sulfate reducer involved in biocorrosion and metal metabolism.Recently, a small group of multisubunit membrane-bound WiFe] hydrogenases has been identified. Sequence analysis of these proteins reveals that they are more closely related to subunits of the proton-pumping NADHquinone oxireductase (complex I) from various organisms than to subunits of other WiFe] hydrogenases (1).To distinguish the istandardi hydrogenases from the multisubunit membrane-bound hydrogenases, the latter have been designated as Eschericbia coli hydrogenase 3-type hydrogenases (1). A group of six genes, encoding a putative multisubunit membrane-bound [NiFe] hydrogenase of the E. coli hydrogenase 3-type was identified in the genome of Desulfovibrio gigas, in addition to the [NiFe] hydrogenase already described for this organism (2). The analysis of sequence data like the search for protein homology, sequence alignment and search for regulatory elements provides insights on the biochemical properties and physiological role of these proteins. In the present study the description of the D. gigas E. coli hydrogenase 3-type hydrogenase operon is reported.