The Origins of Genome Complexity

Lynch, Michael, Conery, John S.·2003·Science
DOI 10.1126/science.1089370

Cited by (1,001)

Items 301–400 of 1,001

  1. A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA
    Carole Knibbe, Antoine Coulon, Olivier Mazet, Jean‐Michel Fayard, Guillaume Beslon · 2007 · Molecular Biology and Evolution
  2. Genomic language model predicts protein co-regulation and function
    Hwang, Yunha, Cornman, Andre L., Kellogg, Elizabeth H., Ovchinnikov, Sergey, Girguis, Peter R. · 2024 · Nature Communications
  3. ALLELIC DIVERGENCE PRECEDES AND PROMOTES GENE DUPLICATION
    Stephen Robert Proulx, Patrick C. Phillips · 2006 · Evolution
  4. Comparative genomics and the evolution of prokaryotes
    Sophie S. Abby, Vincent Daubin · 2007 · Trends in Microbiology
  5. Dynamics of Transcription Factor Binding Site Evolution
    Murat Tuğrul, Tiago Paixão, Nick Barton, Gašper Tkačik · 2015 · PLoS Genetics
  6. The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?
    Claudio Casola, Esther Betrán · 2017 · Genome Biology and Evolution
  7. Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems
    France Denœud, Olivier Godfroy, Corinne Cruaud, Svenja Heesch, Zofia Nehr, Nachida Tadrent, Arnaud Couloux, Loraine Brillet-Guéguen, Ludovic Delage, Dean Mckeown et al. · 2024 · Cell
  8. Group II Introns Break New Boundaries: Presence in a Bilaterian's Genome
    Yvonne Vallès, Kenneth M. Halanych, Jeffrey L. Boore · 2008 · PLoS ONE
  9. Conservative route to genome compaction in a miniature annelid
    José María Martín-Durán, Bruno C. Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetešić, Daniel J. Thiel, Simon Henriet, Xavier Grau‐Bové, Allan M. Carrillo‐Baltodano, Wenjia Gu et al. · 2020 · Nature Ecology & Evolution
  10. The complex relationship of gene duplication and essentiality
    Takashi Makino, Karsten Hokamp, Aoife McLysaght · 2009 · Trends in Genetics
  11. Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis
    Pauline M. Goubet, Hélène Bergès, Arnaud Bellec, Elisa Prat, Nicolas Helmstetter, Sophie Mangenot, Sophie Gallina, Anne-Catherine Holl, Isabelle Fobis‐Loisy, Xavier Vekemans et al. · 2012 · PLoS Genetics
  12. Minireview: Structural and Functional Evolution of the Thyrotropin Receptor
    Nadir R. Farid, Mariusz W. Szkudlinski · 2004 · Endocrinology
  13. A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?
    Kenneth D. Whitney, Eric J. Baack, J. L. Hamrick, Mary Jo W. Godt, Brian C. Barringer, Michael David Bennett, Christopher G. Eckert, Carol Goodwillie, Susan Kalisz, Ilia J. Leitch et al. · 2010 · Evolution
  14. Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing
    Asher D. Cutter, James D. Wasmuth, Nicole L. Washington · 2008 · Genetics
  15. Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs
    David Managadze, Igor B. Rogozin, Diana A. Chernikova, Svetlana A. Shabalina, Eugene V. Koonin · 2011 · Genome Biology and Evolution
  16. Large-Scale Coding Sequence Change Underlies the Evolution of Postdevelopmental Novelty in Honey Bees
    W. Cameron Jasper, Timothy A. Linksvayer, Joel Atallah, Daniel Friedman, Joanna C. Chiu, Brian R. Johnson · 2014 · Molecular Biology and Evolution
  17. Recognizing Student Misconceptions through Ed's Tools and the Biology Concept Inventory
    Michael W. Klymkowsky, Kathy Garvin-Doxas · 2007 · PLoS Biology
  18. STATISTICAL ANALYSIS OF DIVERSIFICATION WITH SPECIES TRAITS
    Emmanuel Paradis · 2005 · Evolution
  19. Widespread Genome Reorganization of an Obligate Virus Mutualist
    Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand · 2014 · PLoS Genetics
  20. Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics
    Adrian W.R. Serohijos, Eugene I. Shakhnovich · 2014 · Current Opinion in Structural Biology
  21. Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels
    Li Jiang, Parul Mishra, Ryan T. Hietpas, Konstantin B. Zeldovich, Daniel N. A. Bolon · 2013 · PLoS Genetics
  22. Genome duplication and gene-family evolution: The case of three OXPHOS gene families
    Anna Grassi, Cecilia Lanave, Cecilia Saccone · 2008 · Gene
  23. Evidence for Abundant Slightly Deleterious Polymorphisms in Bacterial Populations
    Austin L. Hughes · 2004 · Genetics
  24. Stop-codon read-through arises largely from molecular errors and is generally nonadaptive
    Chuan Li, Jianzhi Zhang · 2019 · PLoS Genetics
  25. Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis.
    N. Wickett, L. Honaas, E. Wafula, M. Das, K. Huang, Biao Wu, L. Landherr, M. Timko, J. Yoder, J. Westwood et al. · 2011 · Current Biology
  26. Effective population size and the rate and pattern of nucleotide substitutions
    Megan Woolfit · 2009 · Biology Letters
  27. Evolutionary Capacitance May Be Favored by Natural Selection
    Joanna Masel · 2005 · Genetics
  28. Causes and Consequences of Genome Expansion in Fungi
    Yogeshwar Kelkar, Howard Ochman · 2011 · Genome Biology and Evolution
  29. DNA methylation dynamics at transposable elements in mammals
    Natasha Jansz · 2019 · Essays in Biochemistry
  30. Genic regions of a large salamander genome contain long introns and novel genes
    Jeramiah J. Smith, Srikrishna Putta, Wei Zhu, Gerald M. Pao, Inder M. Verma, Tony R. Hunter, Susan V. Bryant, David M. Gardiner, Timothy T. Harkins, S. Randal Voss · 2009 · BMC Genomics
  31. What We Don't Know About Diet-Breadth Evolution in Herbivorous Insects
    Nate B. Hardy, Chloe Kaczvinsky, Gwendolyn Bird, Benjamin B. Normark · 2020 · Annual Review of Ecology Evolution and Systematics
  32. Role of positive selection in the retention of duplicate genes in mammalian genomes
    Shin‐Han Shiu, Jake Byrnes, Runsun Pan, Peng Zhang, Wen‐Hsiung Li · 2006 · Proceedings of the National Academy of Sciences
  33. Genetic Diversity in the Paramecium aurelia Species Complex
    Francesco Catania, François Wurmser, Alexey A. Potekhin, Ewa Przyboś, Michael Lynch · 2008 · Molecular Biology and Evolution
  34. Symbiogenesis: Mechanisms, Evolutionary Consequences, and Systematic Implications
    Thomas Cavalier‐Smith · 2013 · Annual Review of Ecology Evolution and Systematics
  35. Epistasis and the Adaptability of an RNA Virus
    Rafael Sanjuán, José M. Cuevas, Andrés Moyá, Santiago F. Elena · 2005 · Genetics
  36. A guided tour of large genome size in animals: what we know and where we are heading
    France Dufresne, Nicholas W. Jeffery · 2011 · Chromosome Research
  37. Evolutionarily conserved genes preferentially accumulate introns
    Liran Carmel, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin · 2007 · Genome Research
  38. Translation: The Universal Structural Core of Life
    Chad R. Bernier, Anton S. Petrov, Nicholas A. Kovacs, Petar I. Penev, Loren Dean Williams · 2018 · Molecular Biology and Evolution
  39. Plant Transposable Elements: Biology and Evolution
    Eduard Kejnovský, Jennifer Hawkins, Cédric Feschotte · 2012 · Springer eBooks
  40. Has the connection between polyploidy and diversification actually been tested?
    Elizabeth Anne Kellogg · 2016 · Current Opinion in Plant Biology
  41. The new biology: beyond the Modern Synthesis
    Michael R. Rose, Todd H. Oakley · 2007 · Biology Direct
  42. Phylogeny, Genome Size, and Chromosome Evolution of Asparagales
    Chris Pires, Iván J. Maureira‐Butler, Thomas J. Givnish, Kenneth Systma, Ole Seberg, Gitte Peterson, Jerrold I. Davis, Dennis William Stevenson, Paula J. Rudall, Michael F. Fay et al. · 2006 · Aliso
  43. Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome
    Lu Chen, Jaime M. Tovar-Corona, Araxi O. Urrutia · 2012 · International Journal of Evolutionary Biology
  44. Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome
    Alfredo Villasanté, José P. Abad, María Méndez-Lago · 2007 · Proceedings of the National Academy of Sciences
  45. Quantifying Homologous Replacement of Loci between Haloarchaeal Species
    David F. Williams, Johann Peter Gogarten, R. Thane Papke · 2012 · Genome Biology and Evolution
  46. Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes
    Marc Krasovec, Adam Eyre‐Walker, Sophie Sanchez-Brosseau, Gwenaël Piganeau · 2017 · Molecular Biology and Evolution
  47. Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus
    Sergio M. Latorre, C. Sarai Reyes-Avila, Angus Malmgren, Joe Win, Sophien Kamoun, Hernán A. Burbano · 2020 · BMC Biology
  48. Genome Size: Does Bigger Mean Worse?
    Brian Charlesworth, Nick Barton · 2004 · Current Biology
  49. MATING DENSITY AND THE STRENGTH OF SEXUAL SELECTION AGAINST DELETERIOUS ALLELES INDROSOPHILA MELANOGASTER
    Nathaniel P. Sharp, Aneil F. Agrawal · 2008 · Evolution
  50. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals
    Seung Gu Park, Sridhar S. Hannenhalli, Sun Shim Choi · 2014 · BMC Genomics
  51. Genome-wide functional analysis of human 5' untranslated region introns
    Can Cenik, Adnan Derti, Joseph C. Mellor, Gabriel F. Berriz, Frederick P. Roth · 2010 · Genome biology
  52. The global distribution of angiosperm genome size is shaped by climate
    Petr Bureš, Tammy L. Elliott, Pavel Veselý, Petr Šmarda, Félix Forest, Ilia J. Leitch, Eimear Nic Lughadha, Marybel Soto Gomez, Samuel Pironon, Matilda J. M. Brown et al. · 2024 · New Phytologist
  53. What makes transposable elements move in the Drosophila genome?
    Maria Pilar García Guerreiro · 2011 · Heredity
  54. Origin of introns by ‘intronization’ of exonic sequences
    Manuel Irimia, Jakob Lewin Rukov, David Penny, Jeppe Vinther, Jordi García‐Fernàndez, Scott William Roy · 2008 · Trends in Genetics
  55. Plant Spliceosomal Introns: Not Only Cut and Paste
    Laura Morello, Diego Breviario · 2008 · Current Genomics
  56. Intron-Dominated Genomes of Early Ancestors of Eukaryotes
    Eugene V. Koonin · 2009 · Journal of Heredity
  57. The Evolution of Transcription-Initiation Sites
    Michael Lynch · 2005 · Molecular Biology and Evolution
  58. Genome size evolution: Within-species variation in genome size
    Christian Biémont · 2008 · Heredity
  59. Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes
    Matthew T. Cottrell, David L. Kirchman · 2016 · Applied and Environmental Microbiology
  60. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen
    Fanny E. Hartmann, Daniel Croll · 2017 · Molecular Biology and Evolution
  61. Toward the evaluation of function in genetic variability: Characterizing human SNP frequencies and establishing BAC‐transgenic mice carrying the humanCYP1A1_CYP1A2locus
    Zhengwen Jiang, Timothy P. Dalton, Jin Li, Bin Wang, Yutaka Tsuneoka, Howard G. Shertzer, Ranjan Deka, Daniel W. Nebert · 2005 · Human Mutation
  62. Genome size is negatively correlated with effective population size in ray-finned fish
    Soojin V. Yi, Jeffrey Todd Streelman · 2005 · Trends in Genetics
  63. The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes
    Dareen Almojil, Yann Bourgeois, Marcin Falis, Imtiyaz E. Hariyani, Justin J. S. Wilcox, Stéphane Boissinot · 2021 · Genes
  64. Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis
    Frédéric J. J. Chain, Ben J. Evans · 2006 · PLoS Genetics
  65. Genome Evolution in Reptilia, the Sister Group of Mammals
    Daniel E. Janes, Christopher L. Organ, Matthew K. Fujita, Andrew M. Shedlock, Scott V. Edwards · 2010 · Annual Review of Genomics and Human Genetics
  66. Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum
    Qing Zhang, Weichang Hu, Fan Zhu, Liming Wang, Qingyi Yu, Ray Ming, Jisen Zhang · 2016 · BMC Genomics
  67. Gene duplication in the major insecticide target site, Rdl , in Drosophila melanogaster
    Emily J. Remnant, Robert T. Good, Joshua M. Schmidt, Christopher Lumb, Charles Robin, Phillip J. Daborn, Philip Batterham · 2013 · Proceedings of the National Academy of Sciences
  68. An Interpretive Review of the Origin of Life Research
    David Penny · 2005 · Biology & Philosophy
  69. 50/500 rule and minimum viable populations: response to Jamieson and Allendorf
    Richard Frankham, Barry W. Brook, Corey J. A. Bradshaw, Lochran W. Traill, Derek Spielman · 2013 · Trends in Ecology & Evolution
  70. Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology
    Alexander V. Badyaev · 2011 · Proceedings of the Royal Society B Biological Sciences
  71. Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor
    Sriram G. Garg, William F. Martin · 2016 · Genome Biology and Evolution
  72. Molecular hyperdiversity and evolution in very large populations
    Asher D. Cutter, Richard Jovelin, Alivia Dey · 2013 · Molecular Ecology
  73. The Evolution of Intron Size in Amniotes: A Role for Powered Flight?
    Qu Zhang, Scott V. Edwards · 2012 · Genome Biology and Evolution
  74. High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)
    Kevin L. Vergin, H. James Tripp, Larry Wilhelm, Dee R. Denver, Michael S. Rappé, Stephen J. Giovannoni · 2007 · Environmental Microbiology
  75. The Long Noncoding RNA HOTAIR in Breast Cancer: Does Autophagy Play a Role?
    Elżbieta Pawłowska, Joanna Szczepańska, Janusz Błasiak · 2017 · International Journal of Molecular Sciences
  76. Models of the population genetics of transposable elements
    Arnaud Le Rouzic, Grégory Decelière · 2005 · Genetics Research
  77. Nematode genome evolution
    Avril Coghlan · 2005 · WormBook
  78. Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA
    Julie Nardone, Dong U. Lee, Karl Mark Ansel, Anjana Rao · 2004 · Nature Immunology
  79. Comment on "The Origins of Genome Complexity"
    Vincent Daubin, Nancy A. Moran · 2004 · Science
  80. Mutation rate and genome reduction in endosymbiotic and free-living bacteria
    Gabriel A. B. Marais, Alexandra Calteau, Olivier Tenaillon · 2007 · Genetica
  81. Recombination Drives Vertebrate Genome Contraction
    Kiwoong Nam, Hans Ellegren · 2012 · PLoS Genetics
  82. Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements
    Amir Szitenberg, Soyeon Cha, Charles Opperman, David McK. Bird, Mark Blaxter, David H. Lunt · 2016 · Genome Biology and Evolution
  83. Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century
    Eugene V. Koonin, Kira S. Makarova, Yuri I. Wolf · 2021 · Trends in Microbiology
  84. Parallel evolution of chimeric fusion genes
    Corbin D. Jones, David J Begun · 2005 · Proceedings of the National Academy of Sciences
  85. The mutational hazard hypothesis of organelle genome evolution: 10 years on
    D. Smith · 2016 · Molecular Ecology
  86. Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations
    Shimon Bershtein, Adrian W.R. Serohijos, Eugene I. Shakhnovich · 2016 · Current Opinion in Structural Biology
  87. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi
    Juan Li, Fei Gu, Ru‐Nian Wu, Jinkui Yang, Ke‐Qin Zhang · 2017 · Scientific Reports
  88. The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria
    W. Ran, Paul G. Higgs · 2010 · Molecular Biology and Evolution
  89. Microarray challenges in ecology.
    J. Kammenga, M. A. Herman, N. Ouborg, L. Johnson, R. Breitling · 2007 · Trends in Ecology & Evolution
  90. First Complete Mitochondrial Genome Sequence from a Box Jellyfish Reveals a Highly Fragmented Linear Architecture and Insights into Telomere Evolution
    David Roy Smith, Ehsan Kayal, Angel Anne Yanagihara, Allen Gilbert Collins, S Pirro, Patrick J. Keeling · 2011 · Genome Biology and Evolution
  91. Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome?: A Simulation Study
    Gabriel A. B. Marais, Paulo R. A. Campos, Isabel Gordo · 2010 · Genome Biology and Evolution
  92. Functional Complexity Can Mitigate Performance Trade-Offs
    Roi Holzman, David C. Collar, Rita S. Mehta, Peter C. Wainwright · 2011 · The American Naturalist
  93. Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences.
    L. Rodriguez-R., D. Tsementzi, C. Luo, K. Konstantinidis · 2020 · Environmental Microbiology
  94. In silico experimental evolution: a tool to test evolutionary scenarios
    Bérénice Batut, David P. Parsons, Stephan Fischer, Guillaume Beslon, Carole Knibbe · 2013 · BMC Bioinformatics
  95. Genomic and transcriptomic insights into molecular basis of sexually dimorphic nuptial spines in Leptobrachium leishanense
    Jun Li, Haiyan Yu, Wenxia Wang, Chao Fu, Wei Zhang, Fengming Han, Hua Wu · 2019 · Nature Communications
  96. Unravelling the genome of Holy basil: an “incomparable” “elixir of life” of traditional Indian medicine
    Shubhra Rastogi, Alok Kalra, Vikrant Gupta, Feroz Khan, Raj Kishori Lal, Anil Kumar Tripathi, Sriram Parameswaran, Chellappa Gopalakrishnan, Gopalakrishna Ramaswamy, Ajit Kumar Shasany · 2015 · BMC Genomics
  97. Evolutionary analysis of glycosyl hydrolase family 28 (GH28) suggests lineage-specific expansions in necrotrophic fungal pathogens
    Daniel D. Sprockett, Helen Piontkivska, Christopher B. Blackwood · 2011 · Gene
  98. An Overview of Nested Genes in Eukaryotic Genomes
    Anuj Kumar · 2009 · Eukaryotic Cell
  99. Grammar of protein domain architectures
    Lijia Yu, Deepak K. Tanwar, Emanuel Diego dos Santos Penha, Yuri I. Wolf, Eugene V. Koonin, Malay Kumar Basu · 2019 · Proceedings of the National Academy of Sciences
  100. A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome
    Srinidhi Varadharajan, Pasi M. A. Rastas, Ari Löytynoja, Michael Matschiner, Federico C. F. Calboli, Baocheng Guo, Alexander J. Nederbragt, Kjetill S. Jakobsen, Juha Merilä · 2019 · Genome Biology and Evolution