Fri, 04 Jul 2008 23:39:05 BST CiteULike: Tag lgc http://www.citeulike.org/tag/lgc CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/Ayest/article/1064687 <i>Mamm Genome, Vol. 14, No. 1. (January 2003), pp. 71-80.</i><br /><br />On porcine Chromosome 7, the region surrounding the MHC region contains QTL influencing many traits including growth, back fat thickness, and carcass composition. Towards the identification of the responsible gene(s), this article describes an increase of density of the radiated hybrid map of SSC 7 in the q11-q14 region and the comparative analysis of gene order on the porcine RH map and human genome assembly. Adding 24 new genes in this region, we were able to build a framework map that fills in gaps on the previous maps. The new software Carthagene was used to build a robust framework in this region. Comparative analysis of human and porcine maps revealed a global conservation of gene order and of distances between genes. A rearranged fragment of around 3.7 Mb was, however, found in the pig approximately 20 Mb upstream from the expected location on the basis of the human map. This rearrangement, found by RH mapping on the IMpRH 7.000 rads panel, has been confirmed by two-color FISH and by mapping on the high resolution IMNpRH2 12.000 rads panel. The rearranged fragment contains two microsatellites found at the most likely QTL location in the INRA QTL experiment. It also contains the BMP5 gene, which, together with CLPS, could be considered as a possible candidate. Rearranged gene order between pig and human in a QTL region on SSC 7. O Demeure C Renard M Yerle T Faraut J Riquet A Robic T Schiex A Rink D Milan doi:10.1007/s00335-002-3034-1 Mamm Genome, Vol. 14, No. 1. (January 2003), pp. 71-80. 2007-01-24T08:54:13-00:00 2003 Mamm Genome 0938-8990 14 1 71 80 lgc map porc http://www.citeulike.org/user/Ayest/article/108446 <i>Nucleic Acids Res, Vol. 31, No. 22. (15 November 2003), pp. 6633-6639.</i><br /><br />The advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. Here we describe PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each ENZYME entry. Automatically generated logical rules define which of these profiles is required in order to infer the presence of the corresponding enzyme in an organism. As an example, PRIAM was applied to identify potential metabolic pathways from the complete genome of the nitrogen-fixing bacterium Sinorhizobium meliloti. The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes. Enzyme-specific profiles for genome annotation: PRIAM. C Claudel-Renard C Chevalet T Faraut D Kahn Nucleic Acids Res, Vol. 31, No. 22. (15 November 2003), pp. 6633-6639. 2005-03-01T16:24:36-00:00 2003 Nucleic Acids Res 1362-4962 31 22 6633 6639 lgc pathway http://www.citeulike.org/user/Ayest/article/1064643 <i>Cytogenet Genome Res, Vol. 102, No. 1-4. (2003), pp. 100-108.</i><br /><br />In this study we examined homologies between 1,735 porcine microsatellites and human sequence. For 1,710 microsatellites we directly used the sequence flanking the repeat available in GenBank. For a set of 305 microsatellites, a BAC library was screened and end-sequencing provided 461 additional sequences. Altogether 2,171 porcine sequences were tentatively aligned with the sequence of the human genome using the fasta program. Human homologies were observed for 652 microsatellite loci and porcine chromosome assignments available for 623 microsatellites provide useful links in the human and pig comparative map. Moreover for 92 STS, a significant sequence similarity was detected using at least two sequences and in all cases corresponding human locations were consistent. The present study allowed the integration of anonymous markers and the porcine linkage map into the framework of the comparative data between human and porcine genomes (http://w3.toulouse.inra.fr/lgc/pig/msat/). Moreover all conserved syntenic segments were defined on human chromosomes. A new contribution to the integration of human and porcine genome maps: 623 new points of homology. A Robic T Faraut N Iannuccelli Y Lahbib-Mansais V Cantegrel L Alexander D Milan doi:10.1159/000075733 Cytogenet Genome Res, Vol. 102, No. 1-4. (2003), pp. 100-108. 2007-01-24T08:51:01-00:00 2003 Cytogenet Genome Res 1424-859X 102 1-4 100 108 lgc map porc http://www.citeulike.org/user/Ayest/article/1064640 <i>Cytogenet Genome Res, Vol. 102, No. 1-4. (2003), pp. 109-115.</i><br /><br />A comprehensive and comparative map was constructed for the porcine chromosome (SSC) 6q11-->q21 region, where the gene(s) responsible for the maldevelopment of embryos are localized using swine populations of the National Institute of Animal Industry, Japan (NIAI). Since the chromosomal region corresponds to a region of human chromosome (HSA) 19q13.1-->q13.3 based on bi-directional chromosome painting, primer pairs were designed from porcine cDNA sequences identified, on a sequence comparison basis, as being transcripts from genes orthologous to those in the HSA region. Fifty-one genes were successfully assigned to a swine radiation hybrid (RH) map with LOD scores greater than 6. ERF and PSMD8 genes were assigned to SSC4 and SSC1, respectively. The remaining 49 genes were assigned to SSC6, demonstrating that the synteny between the SSC6 and HSA19 chromosomal regions is essentially conserved, therefore confirming, the results of bi-directional chromosome painting. However, when examined precisely, rearrangements have apparently occurred within the region of conserved synteny. For the ERF and PSMD8 genes assigned to SSCs other than SSC6, additional mapping using somatic cell hybrid (SCH) panels was performed to confirm the results of RH-mapping. Construction of a high-resolution comparative gene map between swine chromosome region 6q11-->q21 and human chromosome 19 q-arm by RH mapping of 51 genes. N Bosak T Faraut S Mikawa H Uenishi S Kiuchi H Hiraiwa T Hayashi H Yasue doi:10.1159/000075734 Cytogenet Genome Res, Vol. 102, No. 1-4. (2003), pp. 109-115. 2007-01-24T08:50:03-00:00 2003 Cytogenet Genome Res 1424-859X 102 1-4 109 115 lgc map porc http://www.citeulike.org/user/Ayest/article/1064634 <i>Mamm Genome, Vol. 15, No. 9. (September 2004), pp. 732-739.</i><br /><br />To validate the ChickRH6 whole-genome radiation hybrid (WGRH) panel, we constructed a map of chicken Chromosome 7 based on 19 microsatellite markers from the genetic map and 76 ESTs (expressed sequence tags), whose efficient targeted development was made possible by using the ICCARE software. This high-density radiation hybrid (RH) map of a chicken macrochromosome gives us indications on characteristics of ChickRH6. The potential resolution of the panel is 325 kb and the practical resolution of our framework map is 1.3 Mb. Based on these results, a complete framework map of the chicken genome would comprise 1000 markers. The marker order is in good agreement with the genetic map and comparison with the human and mouse sequence maps revealed a number of internal rearrangements. Development of a gene-based radiation hybrid map of chicken Chromosome 7 and comparison to human and mouse. M Morisson C Jiguet-Jiglaire S Leroux T Faraut S Bardes K Feve C Genet F Pitel D Milan A Vignal doi:10.1007/s00335-004-3003-y Mamm Genome, Vol. 15, No. 9. (September 2004), pp. 732-739. 2007-01-24T08:49:14-00:00 2004 Mamm Genome 0938-8990 15 9 732 739 chicken lgc mapping