Large-scale trends in the evolution of gene structures within 11 animal genomes

PLoS Computational Biology
M D YandellG M Rubin

Abstract

We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences of five unannotated Drosophila genomes to survey changes in protein sequence and gene structure over a variety of timescales--from the less than 5 million years since the divergence of D. simulans and D. melanogaster to the more than 500 million years that have elapsed since the Cambrian explosion. To do so, we have developed a new open-source software library called CGL (for "Comparative Genomics Library"). Our results demonstrate that change in intron-exon structure is gradual, clock-like, and largely independent of coding-sequence evolution. This means that genome annotations can be used in new ways to inform, corroborate, and test conclusions drawn from comparative genomics analyses that are based upon protein and nucleotide sequence similarities.

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Jun 5, 1991·Journal of Molecular Biology·S F Altschul
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jul 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·B EfronS Holmes
Nov 12, 1996·Proceedings of the National Academy of Sciences of the United States of America·B EfronS Holmes
Jan 1, 1997·Nucleic Acids Research·W M GelbartC Tolstoshev
Oct 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Z ZhangW Miller
Feb 21, 1998·Nucleic Acids Research·UNKNOWN FlyBase Consortium
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·S J de SouzaW Gilbert
Dec 16, 1998·Science·UNKNOWN C. elegans Sequencing Consortium
Feb 10, 2000·Molecular Biology and Evolution·Z Yang, R Nielsen
Mar 24, 2000·Science·G M RubinS Lewis
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Oct 5, 2002·Science·Robert A HoltStephen L Hoffman
Oct 9, 2002·Genome Research·Jason E StajichEwan Birney
Nov 15, 2002·Proceedings of the National Academy of Sciences of the United States of America·Scott William RoyWalter Gilbert
Nov 16, 2002·Current Opinion in Genetics & Development·Michael Lynch, Aaron O Richardson
Dec 6, 2002·Genome Research·Esther BetránManyuan Long
Dec 6, 2002·Nature·UNKNOWN Mouse Genome Sequencing ConsortiumEric S Lander
Apr 10, 2003·Trends in Genetics : TIG·S Blair Hedges, Sudhir Kumar
Sep 2, 2003·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Dec 19, 2003·Nucleic Acids Research·E BirneyT Hubbard
Mar 12, 2004·Molecular Biology and Evolution·Wei-Gang QiuArlin Stoltzfus
May 4, 2004·Current Biology : CB·Arlin Stoltzfus
Jul 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Avril Coghlan, Kenneth H Wolfe
Jul 16, 2004·Nucleic Acids Research·Vladimir N BabenkoEugene V Koonin
Aug 4, 2004·Genome Research·Aleksey Y OgurtsovAlexey S Kondrashov
Sep 10, 2004·Molecular Biology and Evolution·Veiko KraussHeinz Sass
Dec 21, 2004·Nucleic Acids Research·Nansheng ChenLincoln D Stein
Dec 21, 2004·Nucleic Acids Research·Rachel A DrysdaleUNKNOWN FlyBase Consortium
Dec 21, 2004·Nucleic Acids Research·T HubbardE Birney
Mar 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Scott William Roy, Walter Gilbert
May 17, 2005·Genome Biology·Hernán Dopazo, Joaquín Dopazo
May 17, 2005·Genome Biology·Karen EilbeckMichael Ashburner
Jul 17, 2008·Comparative and Functional Genomics·Jay D Evans, Daniel B Weaver

❮ Previous
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Citations

Aug 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Orly Alter, Gene H Golub
Nov 7, 2006·PLoS Computational Biology·Eliot C Bush, Bruce T Lahn
Oct 13, 2007·Science·Sabeeha S MerchantArthur R Grossman
Nov 21, 2007·Genome Research·Brandi L CantarelMark Yandell
Aug 9, 2008·PLoS Computational Biology·Michael SammethRoderic Guigó
Feb 25, 2009·BMC Bioinformatics·Karen EilbeckMark Yandell
May 22, 2009·Genome Research·Michael HillerPeter F Stadler
Jul 29, 2009·The Journal of Heredity·Francesco CataniaDouglas G Scofield
Apr 14, 2010·International Journal of Molecular Sciences·Jean-Yves ExpositoClaire Lethias
Feb 18, 2011·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Barry MooreMark Yandell
Nov 5, 2011·Genome Biology and Evolution·Yuh Chwen G Lee, Josephine A Reinhardt
Oct 30, 2009·Molecular Biology and Evolution·Frida BelinkyDorothée Huchon
Jul 20, 2010·Molecular Biology and Evolution·Nikos AndreakisAnna Palumbo
Nov 28, 2012·Database : the Journal of Biological Databases and Curation·Victor Zeng, Cassandra G Extavour
May 25, 2010·Nucleic Acids Research·Barry MooreKaren Eilbeck
Aug 20, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Michael Sammeth
Aug 11, 2010·Journal of Molecular Evolution·Georgia TsagkogeorgaFrédéric Delsuc
Dec 19, 2012·Theory in Biosciences = Theorie in Den Biowissenschaften·Natascha HillStefanie Hartmann
Dec 7, 2007·Trends in Genetics : TIG·David J Miller, Eldon E Ball
Nov 17, 2011·Wiley Interdisciplinary Reviews. RNA·Katsutomo Okamura
Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gordon GremmeStefan Kurtz
Dec 2, 2006·Gene·Christopher D SmithGary H Karpen
May 3, 2015·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Kasthuri Saranya RevathyJehee Lee
Jul 7, 2015·Molecular Cell·Madalena M Reimão-PintoStefan L Ameres
Oct 30, 2007·Molecular Cell·Eugene BerezikovEric C Lai
Mar 12, 2008·Developmental Cell·Ian A Swinburne, Pamela A Silver
Aug 25, 2006·Genomics·Alaine C KeebaughJames W Thomas
Nov 8, 2014·Frontiers in Endocrinology·Matan GolanBerta Levavi-Sivan
Jan 6, 2017·Cell Cycle·Killeen S KirkconnellMats Ljungman
Jun 26, 2007·Nature·J Graham RubyDavid P Bartel
Jul 25, 2007·Bioinformatics·Christopher J MungallUNKNOWN FlyBase Consortium

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Software Mentioned

RepeatMasker
TBLASTN
Ensembl
CGL
BLASTP
sim4
GadFly
Phylip
BLAST
WU

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