Zagulski M

References (4)

Title : Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia - Aury_2006_Nature_444_171
Author(s) : Aury JM , Jaillon O , Duret L , Noel B , Jubin C , Porcel BM , Segurens B , Daubin V , Anthouard V , Aiach N , Arnaiz O , Billaut A , Beisson J , Blanc I , Bouhouche K , Camara F , Duharcourt S , Guigo R , Gogendeau D , Katinka M , Keller AM , Kissmehl R , Klotz C , Koll F , Le Mouel A , Lepere G , Malinsky S , Nowacki M , Nowak JK , Plattner H , Poulain J , Ruiz F , Serrano V , Zagulski M , Dessen P , Betermier M , Weissenbach J , Scarpelli C , Schachter V , Sperling L , Meyer E , Cohen J , Wincker P
Ref : Nature , 444 :171 , 2006
Abstract : The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.
ESTHER : Aury_2006_Nature_444_171
PubMedSearch : Aury_2006_Nature_444_171
PubMedID: 17086204
Gene_locus related to this paper: parte-a0bds8 , parte-a0bga5 , parte-a0bnp2 , parte-a0bnt1 , parte-a0bpr4 , parte-a0btv5 , parte-a0byt1 , parte-a0bz94 , parte-a0c0b8 , parte-a0c0q4 , parte-a0c1z8 , parte-a0c3e0 , parte-a0c9f4 , parte-a0c962 , parte-a0cb90 , parte-a0cck1 , parte-a0cj40 , parte-a0cq13 , parte-a0cqw8 , parte-a0crq3 , parte-a0cu52 , parte-a0cur9 , parte-a0cxu4 , parte-a0cyf3 , parte-a0czs5 , parte-a0d1l8 , parte-a0d9i7 , parte-a0d589 , parte-a0de29 , parte-a0dem3 , parte-a0dg79 , parte-a0diq2 , parte-a0dk36 , parte-a0dkh0 , parte-a0dld4 , parte-a0dnw2 , parte-a0drp9 , parte-a0drx0 , parte-a0duj9 , parte-a0dvl0 , parte-a0dwm9 , parte-a0dy72 , parte-a0dz74 , parte-a0e0g8 , parte-a0e0z4 , parte-a0e1p0 , parte-a0e4m9 , parte-a0e8v9 , parte-a0e9r1 , parte-a0e581 , parte-a0ecy9 , parte-a0ecz4 , parte-a0ef67 , parte-a0d7k3

Title : High coding density on the largest Paramecium tetraurelia somatic chromosome - Zagulski_2004_Curr.Biol_14_1397
Author(s) : Zagulski M , Nowak JK , Le Mouel A , Nowacki M , Migdalski A , Gromadka R , Noel B , Blanc I , Dessen P , Wincker P , Keller AM , Cohen J , Meyer E , Sperling L
Ref : Current Biology , 14 :1397 , 2004
Abstract : Paramecium, like other ciliates, remodels its entire germline genome at each sexual generation to produce a somatic genome stripped of transposons and other multicopy elements. The germline chromosomes are fragmented by a DNA elimination process that targets heterochromatin to give a reproducible set of some 200 linear molecules 50 kb to 1 Mb in size. These chromosomes are maintained at a ploidy of 800n in the somatic macronucleus and assure all gene expression. We isolated and sequenced the largest megabase somatic chromosome in order to explore its organization and gene content. The AT-rich (72%) chromosome is compact, with very small introns (average size 25 nt), short intergenic regions (median size 202 nt), and a coding density of at least 74%, higher than that reported for budding yeast (70%) or any other free-living eukaryote. Similarity to known proteins could be detected for 57% of the 460 potential protein coding genes. Thirty-two of the proteins are shared with vertebrates but absent from yeast, consistent with the morphogenetic complexity of Paramecium, a long-standing model for differentiated functions shared with metazoans but often absent from simpler eukaryotes. Extrapolation to the whole genome suggests that Paramecium has at least 30,000 genes.
ESTHER : Zagulski_2004_Curr.Biol_14_1397
PubMedSearch : Zagulski_2004_Curr.Biol_14_1397
PubMedID: 15296759
Gene_locus related to this paper: parte-q6bfb1 , parte-q6bfm1 , parte-q6bgf1 , parte-q6bgk8

Title : The sequence of 29.7 kb from the right arm of chromosome II reveals 13 complete open reading frames, of which ten correspond to new genes - Becam_1994_Yeast_10 Suppl A_S1
Author(s) : Becam AM , Cullin C , Grzybowska E , Lacroute F , Nasr F , Ozier-Kalogeropoulos O , Palucha A , Slonimski PP , Zagulski M , Herbert CJ
Ref : Yeast , 10 Suppl A :S1 , 1994
Abstract : We have determined the complete nucleotide sequence of a 29.7 kb segment from the right arm of chromosome II carried by the cosmid alpha 61. The sequence encodes the 3' region of the IRA1 gene and 13 complete open reading frames, of which ten correspond to new genes and three (CIF1, ATPsv and CKS1) have been sequenced previously. The density of protein coding sequences is particularly high and corresponds to 84% of the total length. Two new genes encode membrane proteins, one of which is particularly large, 273 kDa. In one case (ATPsv), the comparison of our sequence and the published sequence reveals significant differences.
ESTHER : Becam_1994_Yeast_10 Suppl A_S1
PubMedSearch : Becam_1994_Yeast_10 Suppl A_S1
PubMedID: 8091856
Gene_locus related to this paper: yeast-yby9

Title : Complete DNA sequence of yeast chromosome II - Feldmann_1994_EMBO.J_13_5795
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
Ref : EMBO Journal , 13 :5795 , 1994
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.
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