Colaniella, foraminifère index du Permien tardif téthysien: propositions pour une taxonomie simplifiée, répartition géographique et environnements

Une classification simplifiee du genre Colaniella LIKHAREV est proposee: Colaniella ex gr. parva, Colaniella ex gr. lepida, Colaniella ex gr. minima. Elle correspond a la division du taxon en trois groupes morphologiques. La repartition geographique de ce taxon est inventoriée de meme que les environnements sedimentaires et les microfaunes associees. Les nouvelles decouvertes de C. ex gr. parva dans Ie Permien superieur des coupes de Mesagros (ile d'Egine, Grece), d'Emarat (N Elbourz, Iran) et du Wadi Wasil dans les montagnes centrales d'Oman sont decrites en detail. L'importance des Colanielles dans la biostratigraphie du Permien superieur tethysien est analysee et clarifiee au vu des travaux recents et Ie problème des migrations est abordé. A simplified taxonomic classification in 3 groups of the genus Colaniella LIKHAREV is proposed: Colaniella ex gr. parva, Colaniella ex gr. lepida, Colaniella ex gr. minima. The repartition of the eight main Colaniella biofacies is given and the paleogeographic distribution of this genus is presented on a late Permian map configuration. New late Permian localities with Colaniella ex gr. parva have been found: Aegina island (Greece), Emmarat in the northern Alborz (Iran) and Wadi Wasit in the central Oman Mountains. The stratigraphic range of Colaniella ex gr. parva is much longer than previously accepted even by specialists. This range begins in the early Midian (Abadehian) and ends in the late Changhsingian (Dorashamian), very close to the range of the genus. For environmental reasons and slow eastward migration we have apparent shorter ranges in the Eastern part of the Tethyan domain.

GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manualannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.Results: The GENCODE gene features are divided into eight different categories of which onlythe first two (known and novel coding sequence) are confidently predicted to be protein-codinggenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentallyverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have beensequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15putative transcripts. We assessed the comprehensiveness of the GENCODE annotation byattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Outof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only twoof them in intergenic regions.Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of theGENCODE reference set available from the UCSC browser. Comparison of GENCODEannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained withinthe two sets, which is a reflection of the high number of alternative splice forms with uniqueexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE forEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% humangenome with the aid of experimental validation.