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Author Report for: Jonniaux JL

Title: The nucleotide sequence of Saccharomyces cerevisiae chromosome IV
Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, Ballesta JP, Bargues M, Baron L, Becker A and Zaccaria P <126 more author(s)> Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, Ballesta JP, Bargues M, Baron L, Becker A, Biteau N, Blocker H, Blugeon C, Boskovic J, Brandt P, Bruckner M, Buitrago MJ, Coster F, Delaveau T, del Rey F, Dujon B, Eide LG, Garcia-Cantalejo JM, Goffeau A, Gomez-Peris AC, Granotier C, Hanemann V, Hankeln T, Hoheisel JD, Jager W, Jimenez A, Jonniaux JL, Kramer C, Kuster H, Laamanen P, Legros Y, Louis E, Muller-Rieker S, Monnet A, Moro M, Muller-Auer S, Nussbaumer B, Paricio N, Paulin L, Perea J, Perez-Alonso M, Perez-Ortin JE, Pohl TM, Prydz H, Purnelle B, Rasmussen SW, Remacha M, Revuelta JL, Rieger M, Salom D, Saluz HP, Saiz JE, Saren AM, Schafer M, Scharfe M, Schmidt ER, Schneider C, Scholler P, Schwarz S, Soler-Mira A, Urrestarazu LA, Verhasselt P, Vissers S, Voet M, Volckaert G, Wagner G, Wambutt R, Wedler E, Wedler H, Wolfl S, Harris DE, Bowman S, Brown D, Churcher CM, Connor R, Dedman K, Gentles S, Hamlin N, Hunt S, Jones L, McDonald S, Murphy L, Niblett D, Odell C, Oliver K, Rajandream MA, Richards C, Shore L, Walsh SV, Barrell BG, Dietrich FS, Mulligan J, Allen E, Araujo R, Aviles E, Berno A, Carpenter J, Chen E, Cherry JM, Chung E, Duncan M, Hunicke-Smith S, Hyman R, Komp C, Lashkari D, Lew H, Lin D, Mosedale D, Nakahara K, Namath A, Oefner P, Oh C, Petel FX, Roberts D, Schramm S, Schroeder M, Shogren T, Shroff N, Winant A, Yelton M, Botstein D, Davis RW, Johnston M, Hillier L, Riles L, Albermann K, Hani J, Heumann K, Kleine K, Mewes HW, Zollner A, Zaccaria P (- 126)
Ref: Nature, 387:75, 1997 : PubMed
Abstract


ESTHER: Jacq_1997_Nature_387_75
PubMedSearch: Jacq 1997 Nature 387 75
PubMedID: 9169867
Gene_locus related to this paper: yeast-dlhh, yeast-ECM18, yeast-YDL109C, yeast-YDR428C, yeast-YDR444W

Abstract

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.



        

Title: The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications
Philippsen P, Kleine K, Pohlmann R, Dusterhoft A, Hamberg K, Hegemann JH, Obermaier B, Urrestarazu LA, Aert R and Hani J <78 more author(s)> Philippsen P, Kleine K, Pohlmann R, Dusterhoft A, Hamberg K, Hegemann JH, Obermaier B, Urrestarazu LA, Aert R, Albermann K, Altmann R, Andre B, Baladron V, Ballesta JP, Becam AM, Beinhauer J, Boskovic J, Buitrago MJ, Bussereau F, Coster F, Crouzet M, D'Angelo M, Dal Pero F, De Antoni A, del Rey F, Doignon F, Domdey H, Dubois E, Fiedler T, Fleig U, Floeth M, Fritz C, Gaillardin C, Garcia-Cantalejo JM, Glansdorff NN, Goffeau A, Gueldener U, Herbert C, Heumann K, Heuss-Neitzel D, Hilbert H, Hinni K, Iraqui Houssaini I, Jacquet M, Jimenez A, Jonniaux JL, Karpfinger L, Lanfranchi G, Lepingle A, Levesque H, Lyck R, Maftahi M, Mallet L, Maurer KC, Messenguy F, Mewes HW, Mosti D, Nasr F, Nicaud JM, Niedenthal RK, Pandolfo D, Pierard A, Piravandi E, Planta RJ, Pohl TM, Purnelle B, Rebischung C, Remacha M, Revuelta JL, Rinke M, Saiz JE, Sartorello F, Scherens B, Sen-Gupta M, Soler-Mira A, Urbanus JH, Valle G, van Dyck L, Verhasselt P, Vierendeels F, Vissers S, Voet M, Volckaert G, Wach A, Wambutt R, Wedler H, Zollner A, Hani J (- 78)
Ref: Nature, 387:93, 1997 : PubMed
Abstract


ESTHER: Philippsen_1997_Nature_387_93
PubMedSearch: Philippsen 1997 Nature 387 93
PubMedID: 9169873
Gene_locus related to this paper: yeast-SCYNR064C, yeast-hda1

Abstract

In 1992 we started assembling an ordered library of cosmid clones from chromosome XIV of the yeast Saccharomyces cerevisiae. At that time, only 49 genes were known to be located on this chromosome and we estimated that 80% to 90% of its genes were yet to be discovered. In 1993, a team of 20 European laboratories began the systematic sequence analysis of chromosome XIV. The completed and intensively checked final sequence of 784,328 base pairs was released in April, 1996. Substantial parts had been published before or had previously been made available on request. The sequence contained 419 known or presumptive protein-coding genes, including two pseudogenes and three retrotransposons, 14 tRNA genes, and three small nuclear RNA genes. For 116 (30%) protein-coding sequences, one or more structural homologues were identified elsewhere in the yeast genome. Half of them belong to duplicated groups of 6-14 loosely linked genes, in most cases with conserved gene order and orientation (relaxed interchromosomal synteny). We have considered the possible evolutionary origins of this unexpected feature of yeast genome organization.



        

Title: Complete DNA sequence of yeast chromosome II
Feldmann H, Aigle M, Aljinovic G, Andre B, Baclet MC, Barthe C, Baur A, Becam AM, Biteau N and Schaaff-Gerstenschlger I <91 more author(s)> Feldmann H, Aigle M, Aljinovic G, Andre B, Baclet MC, Barthe C, Baur A, Becam AM, Biteau N, Boles E, Brandt T, Brendel M, Bruckner M, Bussereau F, Christiansen C, Contreras R, Crouzet M, Cziepluch C, Demolis N, Delaveau T, Doignon F, Domdey H, Dusterhus S, Dubois E, Dujon B, El Bakkoury M, Entian KD, Feurmann M, Fiers W, Fobo GM, Fritz C, Gassenhuber H, Glandsdorff N, Goffeau A, Grivell LA, de Haan M, Hein C, Herbert CJ, Hollenberg CP, Holmstrom K, Jacq C, Jacquet M, Jauniaux JC, Jonniaux JL, Kallesoe T, Kiesau P, Kirchrath L, Kotter P, Korol S, Liebl S, Logghe M, Lohan AJ, Louis EJ, Li ZY, Maat MJ, Mallet L, Mannhaupt G, Messenguy F, Miosga T, Molemans F, Muller S, Nasr F, Obermaier B, Perea J, Pierard A, Piravandi E, Pohl FM, Pohl TM, Potier S, Proft M, Purnelle B, Ramezani Rad M, Rieger M, Rose M, Schaaff-Gerstenschlager I, Scherens B, Schwarzlose C, Skala J, Slonimski PP, Smits PH, Souciet JL, Steensma HY, Stucka R, Urrestarazu A, van der Aart QJ, van Dyck L, Vassarotti A, Vetter I, Vierendeels F, Vissers S, Wagner G, de Wergifosse P, Wolfe KH, Zagulski M, Zimmermann FK, Mewes HW, Kleine K, Dsterhus S, Mller S, Pirard A, Schaaff-Gerstenschlger I (- 91)
Ref: EMBO Journal, 13:5795, 1994 : PubMed
Abstract


ESTHER: Feldmann_1994_EMBO.J_13_5795
PubMedSearch: Feldmann 1994 EMBO.J 13 5795
PubMedID: 7813418
Gene_locus related to this paper: yeast-LDH1, yeast-MCFS2, yeast-yby9

Abstract

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.