Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy.

The Plant Cell
Christopher D TownIan Bancroft

Abstract

We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea, which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis thaliana genome. Sequence annotation identified 177 conserved collinear genes in the B. oleracea genome segments. Analysis of synonymous base substitution rates indicated that the triplicated Brassica genome segments diverged from a common ancestor soon after divergence of the Arabidopsis and Brassica lineages. This conclusion was corroborated by phylogenetic analysis of protein families. Using A. thaliana as an outgroup, 35% of the genes inferred to be present when genome triplication occurred in the Brassica lineage have been lost, most likely via a deletion mechanism, in an interspersed pattern. Genes encoding proteins involved in signal transduction or transcription were not found to be significantly more extensively retained than those encoding proteins classified with other functions, but putative proteins predicted in the A. thaliana genome were underrepresented in B. oleracea. We identified one example of gene loss from the Arabidopsis lineage. We found evidence for the frequent insertion of gene fragments of nuclear genomic o...Continue Reading

References

Aug 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·K H WolfeW H Li
Aug 15, 1995·Proceedings of the National Academy of Sciences of the United States of America·K SongT C Osborn
Dec 1, 1996·Genetics·U Lagercrantz, D J Lydiate
Apr 25, 1997·Journal of Molecular Biology·C Burge, S Karlin
Dec 24, 1997·Genomics·X HuangA R Kerlavage
Mar 21, 1998·Nucleic Acids Research·A V Lukashin, M Borodovsky
Jul 9, 1999·Genomics·S L SalzbergH Tettelin
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Dec 11, 1999·Nucleic Acids Research·J QuackenbushJ Upton
Jul 19, 2000·The Plant Cell·G BlancM Delseny
Jul 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·H M KuS D Tanksley
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Feb 15, 2001·Trends in Genetics : TIG·I Bancroft
Feb 27, 2001·Nucleic Acids Research·M PerteaS L Salzberg
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
May 2, 2003·Genome Génome / Conseil National De Recherches Canada·I A P ParkinD J Lydiate
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 23, 2004·The Plant Cell·Guillaume Blanc, Kenneth H Wolfe
Jul 21, 2004·Briefings in Bioinformatics·Sudhir KumarMasatoshi Nei
Jul 31, 2004·Genome Génome / Conseil National De Recherches Canada·Muqiang GaoCarlos F Quiros
Oct 1, 2004·Nature·Ning JiangSusan R Wessler
Nov 18, 2004·The Plant Journal : for Cell and Molecular Biology·Debashis RanaIan Bancroft
Mar 23, 2005·Genome Research·Martin A LysakIngo Schubert
Apr 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Steven MaereYves Van de Peer
Jun 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jinsheng LaiHugo K Dooner
Aug 16, 2005·Nature·UNKNOWN International Rice Genome Sequencing Project
Dec 1, 1995·Genome Génome / Conseil National De Recherches Canada·I A ParkinD J Lydiate
Jul 1, 1991·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·S I Warwick, L D Black

❮ Previous
Next ❯

Citations

Dec 6, 2008·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Goro IshikawaTakashi Matsumoto
Jan 10, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Edward HimelblauGeorge W Haughn
Nov 19, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Nataša FormanováGregory G Brown
Jan 21, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Juliane MittaschCarsten Milkowski
Feb 13, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xiaoling SongSheng Qiang
Dec 25, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·A M SmookerI Bancroft
Jul 16, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Congcong JiangJinling Meng
Dec 27, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hans-Joachim HarloffChristian Jung
Jan 14, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Pablo D CárdenasMaría L Federico
Mar 3, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Ji LiGuangsheng Yang
Sep 6, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·David EdwardsRod J Snowdon
Dec 15, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Haitao LiKede Liu
Oct 20, 2009·Molecular Genetics and Genomics : MGG·Jeong-Hwan MunBeom-Seok Park
Dec 22, 2009·Molecular Genetics and Genomics : MGG·Soomin ParkSeung-Chan Lee
Feb 14, 2007·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Rod J Snowdon
Sep 28, 2007·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Xian-Hong Ge, Zai-Yun Li
Aug 2, 2011·Nature Biotechnology·Ian BancroftMartin Trick
Jul 24, 2012·Nature Biotechnology·Andrea L HarperIan Bancroft
Aug 30, 2011·Nature Genetics·Xiaowu WangUNKNOWN Brassica rapa Genome Sequencing Project Consortium
Jul 13, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hiroshi AbeMasatomo Kobayashi
Aug 6, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Feng LiTakeshi Nishio
Nov 8, 2011·Genome Biology and Evolution·Corey M HudsonGavin C Conant
Oct 10, 2008·Molecular Biology and Evolution·Martin A LysakIlia J Leitch
Mar 24, 2009·Nucleic Acids Research·Piotr A ZiolkowskiJan Sadowski
Apr 22, 2010·Plant Physiology·Xiaodong XuC Robertson McClung
Aug 21, 2007·The Plant Cell·Claudia KutterAzeddine Si-Ammour
Jul 20, 2010·The Plant Cell·Terezie MandákováMartin A Lysak
Mar 22, 2008·Genome Génome / Conseil National De Recherches Canada·Keita SuwabeIan Bancroft
Sep 22, 2009·Genome Génome / Conseil National De Recherches Canada·Malgorzata KaczmarekJan Sadowski
Feb 5, 2010·Genome Génome / Conseil National De Recherches Canada·Swarup K ParidaTrilochan Mohapatra

❮ Previous
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