The collapse of gene complement following whole genome duplication

被引:89
作者
Sankoff, David [1 ]
Zheng, Chunfang [2 ]
Zhu, Qian [3 ]
机构
[1] Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada
[2] Univ Montreal, Dept Informat & Rech Operat, Montreal, PQ H3C 3J7, Canada
[3] Princeton Univ, Dept Comp Sci, Princeton, NJ 08544 USA
来源
BMC GENOMICS | 2010年 / 11卷
基金
加拿大自然科学与工程研究理事会;
关键词
REVEALS; REORGANIZATION; RECONSTRUCTION; ARABIDOPSIS; EVOLUTION; FATE;
D O I
10.1186/1471-2164-11-313
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an inexorable collapse in gene complement. Results: We compare fifteen genomes descending from six eukaryotic WGD events 20-450 Mya. We characterize the collapse over time through the distribution of runs of reduced paralog pairs in duplicated segments. Descendant genomes of the same WGD event behave as replicates. Choice of paralog pairs to be reduced is random except for some resistant regions of contiguous pairs. For those paralog pairs that are reduced, conserved copies tend to concentrate on one chromosome. Conclusions: Both the contiguous regions of reduction-resistant pairs and the concentration of runs of single copy genes on a single chromosome are evidence of transcriptional co-regulation, dosage sensitivity or other functional interaction constraining the reduction process. These constraints and their evolution over time show a consistent pattern across evolutionary domains and a highly reproducible pattern, as replicates, for the several descendants of a single WGD.
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页数:11
相关论文
共 23 条
[1]   Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia [J].
Aury, Jean-Marc ;
Jaillon, Olivier ;
Duret, Laurent ;
Noel, Benjamin ;
Jubin, Claire ;
Porcel, Betina M. ;
Segurens, Beatrice ;
Daubin, Vincent ;
Anthouard, Veronique ;
Aiach, Nathalie ;
Arnaiz, Olivier ;
Billaut, Alain ;
Beisson, Janine ;
Blanc, Isabelle ;
Bouhouche, Khaled ;
Camara, Francisco ;
Duharcourt, Sandra ;
Guigo, Roderic ;
Gogendeau, Delphine ;
Katinka, Michael ;
Keller, Anne-Marie ;
Kissmehl, Roland ;
Klotz, Catherine ;
Koll, France ;
Le Mouel, Anne ;
Lepere, Gersende ;
Malinsky, Sophie ;
Nowacki, Mariusz ;
Nowak, Jacek K. ;
Plattner, Helmut ;
Poulain, Julie ;
Ruiz, Francoise ;
Serrano, Vincent ;
Zagulski, Marek ;
Dessen, Philippe ;
Betermier, Mireille ;
Weissenbach, Jean ;
Scarpelli, Claude ;
Schaechter, Vincent ;
Sperling, Linda ;
Meyer, Eric ;
Cohen, Jean ;
Wincker, Patrick .
NATURE, 2006, 444 (7116) :171-178
[2]   Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events [J].
Bowers, JE ;
Chapman, BA ;
Rong, JK ;
Paterson, AH .
NATURE, 2003, 422 (6930) :433-438
[3]   The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species [J].
Byrne, KP ;
Wolfe, KH .
GENOME RESEARCH, 2005, 15 (10) :1456-1461
[4]   Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion [J].
Byrnes, Jake K. ;
Morris, Geoffrey P. ;
Li, Wen-Hsiung .
MOLECULAR BIOLOGY AND EVOLUTION, 2006, 23 (06) :1136-1143
[5]   Two rounds of whole genome duplication in the ancestral vertebrate [J].
Dehal, P ;
Boore, JL .
PLOS BIOLOGY, 2005, 3 (10) :1700-1708
[6]   A sense of self: The role of DNA sequence elimination in allopolyploidization [J].
Eckardt, NA .
PLANT CELL, 2001, 13 (08) :1699-1704
[7]   Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes [J].
Edger, Patrick P. ;
Pires, J. Chris .
CHROMOSOME RESEARCH, 2009, 17 (05) :699-717
[8]   Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome [J].
Gordon, Jonathan L. ;
Byrne, Kevin P. ;
Wolfe, Kenneth H. .
PLOS GENETICS, 2009, 5 (05)
[9]  
GUAN Y, 2003, SIAM J COMPUT, V32, P754
[10]   Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype [J].
Jaillon, O ;
Aury, JM ;
Brunet, F ;
Petit, JL ;
Stange-Thomann, N ;
Mauceli, E ;
Bouneau, L ;
Fischer, C ;
Ozouf-Costaz, C ;
Bernot, A ;
Nicaud, S ;
Jaffe, D ;
Fisher, S ;
Lutfalla, G ;
Dossat, C ;
Segurens, B ;
Dasilva, C ;
Salanoubat, M ;
Levy, M ;
Boudet, N ;
Castellano, S ;
Anthouard, R ;
Jubin, C ;
Castelli, V ;
Katinka, M ;
Vacherie, B ;
Biémont, C ;
Skalli, Z ;
Cattolico, L ;
Poulain, J ;
de Berardinis, V ;
Cruaud, C ;
Duprat, S ;
Brottier, P ;
Coutanceau, JP ;
Gouzy, J ;
Parra, G ;
Lardier, G ;
Chapple, C ;
McKernan, KJ ;
McEwan, P ;
Bosak, S ;
Kellis, M ;
Volff, JN ;
Guigó, R ;
Zody, MC ;
Mesirov, J ;
Lindblad-Toh, K ;
Birren, B ;
Nusbaum, C .
NATURE, 2004, 431 (7011) :946-957