The origins of genome complexity

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

Cited by (1,002)

Items 401–500 of 1,002

  1. Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number
    Scott William Roy, Daniel L. Hartl · 2006 · Genome Research
  2. Phenotype inference in an Escherichia coli strain panel
    Marco Galardini, Alexandra Koumoutsi, Lucía Herrera-Domínguez, Juan Antonio Cordero Varela, Anja Telzerow, Omar Wagih, Morgane Wartel, Olivier Clermont, Érick Denamur, Athanasios Typas et al. · 2017 · eLife
  3. Intron and gene size expansion during nervous system evolution
    Matthew J. McCoy, Andrew Z. Fire · 2020 · BMC Genomics
  4. Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes
    Sankar Subramanian · 2008 · Genetics
  5. Simplicity and Complexity of Microsporidian Genomes
    Patrick J. Keeling, Claudio H. Slamovits · 2004 · Eukaryotic Cell
  6. Weighing the evidence for adaptation at the molecular level
    Justin C. Fay · 2011 · Trends in Genetics
  7. Rate variation between mitochondrial domains and adaptive evolution in humans
    Max Ingman, Ulf B Gyllensten · 2007 · Human Molecular Genetics
  8. The economics of organellar gene loss and endosymbiotic gene transfer
    Kelly, Steven · 2021 · Genome Biology
  9. Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity
    Inmaculada Yruela, Christopher J. Oldfield, Karl Joseph Niklas, A. Keith Dunker · 2017 · Genome Biology and Evolution
  10. The Ingenuity of Bacterial Genomes
    Paul C. Kirchberger, Marian L. Schmidt, Howard Ochman · 2020 · Annual Review of Microbiology
  11. The transposable element-rich genome of the cereal pest Sitophilus oryzae
    Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Bâa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet et al. · 2021 · BMC Biology
  12. The impact of long-distance horizontal gene transfer on prokaryotic genome size
    Otto X. Cordero, Paulien Hogeweg · 2009 · Proceedings of the National Academy of Sciences
  13. CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)1
    Jessica A. Connolly, Matthew John Oliver, Jeremy M. Beaulieu, Charles A. Knight, Lars Tomanek, Mark A. Moline · 2008 · Journal of Phycology
  14. Functional and Evolutionary Analysis of the Genome of an Obligate Fungal Symbiont
    Kevin J. Vogel, Nancy A. Moran · 2013 · Genome Biology and Evolution
  15. Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
    Yang Liu, Qian Liu, Handong Su, Kunpeng Liu, Xue Xiao, Wei Li, Qianwen Sun, James A. Birchler, Fangpu Han · 2021 · Genome Research
  16. Evolution of sex and mating loci: An expanded view from Volvocine algae
    James Umen · 2011 · Current Opinion in Microbiology
  17. How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner
    J. Vollmers, Sandra Wiegand, Florian Lenk, A. Kaster · 2022 · Nucleic Acids Research
  18. Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data
    Mark C. Ungerer, Suzanne C. Strakosh, Kaitlin M. Stimpson · 2009 · BMC Biology
  19. Unexpected Diversity and Differential Success of DNA Transposons in Four Species of Entamoeba Protozoans
    Ellen J. Pritham, Cédric Feschotte, Susan R. Wessler · 2005 · Molecular Biology and Evolution
  20. Evolution of genome size: multilevel selection, mutation bias or dynamical chaos?
    Alexander E. Vinogradov · 2004 · Current Opinion in Genetics & Development
  21. Mutation–selection balance and compensatory mechanisms in tumour evolution
    Erez Persi, Yuri I. Wolf, D. Horn, Eytan Ruppin, Francesca Demichelis, Robert A. Gatenby, Robert J. Gillies, Eugene V. Koonin · 2020 · Nature Reviews Genetics
  22. Genome size evolution in the diverse insect order Trichoptera
    Jacqueline Heckenhauer, Paul B. Frandsen, John S. Sproul, Zheng Li, Juraj Paule, Amanda M. Larracuente, Peter J. Maughan, Michael S. Barker, Julio V. Schneider, Russell J. Stewart et al. · 2022 · GigaScience
  23. Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in L iliaceae
    Angelino Carta, Lorenzo Peruzzi · 2015 · New Phytologist
  24. Adaptation in plant genomes: Bigger is different
    Wenbin Mei, Markus G Stetter, Daniel J. Gates, Michelle C. Stitzer, Jeffrey Ross‐Ibarra · 2018 · American Journal of Botany
  25. Comprehensive database and evolutionary dynamics of U12-type introns
    Devlin C. Moyer, Graham E. Larue, Courtney E. Hershberger, Scott William Roy, Richard A. Padgett · 2020 · Nucleic Acids Research
  26. Single-molecule analysis of nucleic acid biomarkers – A review
    Tal Gilboa, Padric M. Garden, Limor Cohen · 2020 · Analytica Chimica Acta
  27. Selection on Major Components of Angiosperm Genomes
    Brandon S. Gaut, Jeffrey Ross‐Ibarra · 2008 · Science
  28. Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory
    Asher D. Cutter · 2013 · Molecular Phylogenetics and Evolution
  29. Extensive Proliferation of Transposable Elements in Heritable Bacterial Symbionts
    Gordon R. Plague, Helen E. Dunbar, Phat L Tran, Nancy A. Moran · 2007 · Journal of Bacteriology
  30. Nitrogen limitation as a driver of genome size evolution in a group of karst plants
    Ming Kang, Jing Wang, Hongwen Huang · 2015 · Scientific Reports
  31. Protein material costs: single atoms can make an evolutionary difference
    Jason G. Bragg, Andreas Wagner · 2008 · Trends in Genetics
  32. Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity
    Lisa L. Ellis, Wen Huang, Andrew M. Quinn, Astha Ahuja, Ben Alfrejd, Francisco E. Gomez, Carl E. Hjelmen, Kristi L. Moore, Trudy F. C. Mackay, J. Spencer Johnston et al. · 2014 · PLoS Genetics
  33. Mining plant diversity: Gerbera as a model system for plant developmental and biosynthetic research
    Teemu H. Teeri, Paula Elomaa, Mika Kotilainen, Victor A. Albert · 2006 · BioEssays
  34. Endosymbiosis and its implications for evolutionary theory
    Maureen A. O’Malley · 2015 · Proceedings of the National Academy of Sciences
  35. On the Origin of the Eukaryotic Chromosome: The Role of Noncanonical DNA Structures in Telomere Evolution
    Miguel Garavís, Carlos González, Alfredo Villasanté · 2013 · Genome Biology and Evolution
  36. Pleiotropic functions of a conserved insect-specific Hox peptide motif
    Chris Todd Hittinger, David L. Stern, Sean B. Carroll · 2005 · Development
  37. The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions
    Vincent Mérel, Patricia Gibert, Inessa Buch, Valentina Rodriguez Rada, Arnaud Estoup, Mathieu Gautier, Marie Fablet, Matthieu Boulesteix, Cristina P Vieira · 2021 · Molecular Biology and Evolution
  38. Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae
    David Eduardo Torres, Bart P. H. J. Thomma, Michael F. Seidl · 2021 · Genome Biology and Evolution
  39. Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation
    Christopher D. Reinkemeier, Edward A. Lemke · 2021 · Cell
  40. Insect Juvenile Hormone Binding Protein Shows Ancestral Fold Present in Human Lipid-Binding Proteins
    R. Kolodziejczyk, Grzegorz Bujacz, Michał Jakób, Andrzej Ożyhar, Mariusz Jaskólski, Marian Kochman · 2008 · Journal of Molecular Biology
  41. Patterns of genome size diversity in the ray-finned fishes
    Smith, Emily M., Gregory, T. Ryan · 2009 · Hydrobiologia
  42. Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes
    Emmanuelle Lerat, Nelly Burlet, Christian Biémont, Cristina P Vieira · 2010 · Gene
  43. Genome evolution mediated by Ty elements in Saccharomyces
    David J Garfinkel · 2005 · Cytogenetic and Genome Research
  44. Selfish Little Circles: Transmission Bias and Evolution of Large Deletion-Bearing Mitochondrial DNA in Caenorhabditis briggsae Nematodes
    Katie A. Clark, Dana K. Howe, Kristin Gafner, Danika N. Kusuma, Sita Ping, Suzanne Estes, Dee R. Denver · 2012 · PLoS ONE
  45. The meaning of biological information
    Eugene V. Koonin · 2016 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
  46. Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy
    Junkang Rong, John Bowers, Stefan R. Schulze, Vijay Namdeo Waghmare, Carl J. Rogers, Gary J. Pierce, Hua Zhang, James C. Estill, Andrew H. Paterson · 2005 · Genome Research
  47. Transcriptional fates of human-specific segmental duplications in brain
    Max L. Dougherty, Jason G. Underwood, Bradley J. Nelson, Elizabeth Tseng, Katherine M. Munson, Osnat Penn, Tomasz Jan Nowakowski, Alex A. Pollen, Evan E. Eichler · 2018 · Genome Research
  48. The economics of organellar gene loss and endosymbiotic gene transfer
    Kelly, Steven · 2020
  49. Conserved non-coding elements and cis regulation: actions speak louder than words
    Andrew C. Nelson, Fiona C. Wardle · 2013 · Development
  50. Protein subcellular relocalization: a new perspective on the origin of novel genes
    S. McKay, R. Geeta · 2007 · Trends in Ecology & Evolution
  51. Low nucleotide diversity for the expanded organelle and nuclear genomes of Volvox carteri supports the mutational-hazard hypothesis.
    D. Smith, Robert W. Lee · 2010 · Molecular biology and evolution
  52. Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness
    Tobias Sikosek, Hue Sun Chan, Erich Bornberg‐Bauer · 2012 · Proceedings of the National Academy of Sciences
  53. Evolution on the Biophysical Fitness Landscape of an RNA Virus
    Assaf Rotem, Adrian W.R. Serohijos, Connie B. Chang, Joshua T. Wolfe, Audrey E. Fischer, Thomas S. Mehoke, Huidan Zhang, Ye Tao, W. Lloyd Ung, Jeong‐Mo Choi et al. · 2018 · Molecular Biology and Evolution
  54. The evolution of neuroendocrine peptides
    John Michael Conlon, Dan Larhammar · 2005 · General and Comparative Endocrinology
  55. Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Jinhui Shen, Qian Cong, Lisa N. Kinch, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin · 2016 · F1000Research
  56. No Gene-Specific Optimization of Mutation Rate in Escherichia coli
    Xiao Chen, J. Zhang · 2013 · Molecular Biology and Evolution
  57. Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle
    Haiwei Fan, Hiroaki Noda, Hongqing Xie, Yoshitaka Suetsugu, Qianhua Zhu, Chuan‐Xi Zhang · 2015 · Genome Biology and Evolution
  58. Codon Usage and Selection on Proteins
    Joshua B. Plotkin, Jonathan G. Dushoff, Michael M. Desai, Hunter B. Fraser · 2006 · Journal of Molecular Evolution
  59. The Influence of Selection for Protein Stability on dN/dS Estimations
    Pouria Dasmeh, Adrian W.R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich · 2014 · Genome Biology and Evolution
  60. Macroevolution and the Genome
    T. Ryan Gregory · 2005 · Elsevier eBooks
  61. Transposable Elements
    MARGARET GALE KIDWELL · 2005 · Elsevier eBooks
  62. Introduction to Systems Biology
    Bin Hu, Pawan Kumar Dhar · 2014 · Springer eBooks
  63. Organelle genome complexity scales positively with organism size in volvocine green algae.
    D. Smith, Takashi Hamaji, B. J. Olson, Pierre M. Durand, P. Ferris, R. Michod, J. Featherston, H. Nozaki, P. Keeling · 2013 · Molecular biology and evolution
  64. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
    Nicole de la Chaux, Takashi Tsuchimatsu, Kentaro K. Shimizu, Andreas Wagner · 2012 · Mobile DNA
  65. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
    Jaqueline Hess, Inger Skrede, Benjamin E. Wolfe, Kurt M. LaButti, Robin A. Ohm, Igor V. Grigoriev, Anne Pringle · 2014 · Genome Biology and Evolution
  66. Disentangling the effects of selection and loss bias on gene dynamics
    Jaime Iranzo, José A. Cuesta, Susanna C. Manrubia, Mikhail I. Katsnelson, Eugene V. Koonin · 2017 · Proceedings of the National Academy of Sciences
  67. Rapid divergence and diversification of mammalian duplicate gene functions
    Raquel Assis, Doris Bachtrog · 2015 · BMC Evolutionary Biology
  68. Whence genes in pieces: reconstruction of the exon–intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes
    Eugene V. Koonin, Miklós Csürös, Igor B. Rogozin · 2012 · Wiley Interdisciplinary Reviews - RNA
  69. Opsins: Evolution in Waiting
    Ann E. O. Trezise, Shaun P. Collin · 2005 · Current Biology
  70. Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes
    Jean‐Luc Da Lage, Manfred Binder, Aurélie Hua‐Van, Ŝtefan Janeĉek, Didier Casañe · 2013 · BMC Evolutionary Biology
  71. Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability
    Han Liang, Kristina Rogale, Jianping Chen, Wen‐Hsiung Li, Ariel Fernández · 2008 · PLoS Genetics
  72. The genomics of adaptation
    Jacek Radwan, Wiesław Babik · 2012 · Proceedings of the Royal Society B Biological Sciences
  73. Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales
    Carolina A. Martínez-Gutiérrez, Frank O. Aylward · 2022 · PLoS Genetics
  74. The evolution of animal genomes
    Casey W. Dunn, Joseph F. Ryan · 2015 · Current Opinion in Genetics & Development
  75. Competition may determine the diversity of transposable elements
    György Abrusán, Hans-Jürgen Krambeck · 2006 · Theoretical Population Biology
  76. Effects of metabolic rate on protein evolution
    James F. Gillooly, Michael W. McCoy, Andrew Paul Allen · 2007 · Biology Letters
  77. Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes
    Jun Wang, Nicholas C. Marowsky, Chuanzhu Fan · 2014 · PLoS ONE
  78. Relationship between genome size and organismal complexity in the lineage leading from prokaryotes to mammals
    Alexander V Markov, В.А. Анисимов, Andrey Korotayev · 2010 · Paleontological Journal
  79. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach
    Ajna S. Rivera, M. Sabrina Pankey, David C. Plachetzki, Carlos Villacorta Martin, Anna Syme, Jeanne M. Serb, Angela R. Omilian, Todd H. Oakley · 2010 · BMC Evolutionary Biology
  80. How does selfing affect the dynamics of selfish transposable elements?
    Thibaud Boutin, Arnaud Le Rouzic, Pierre Capy · 2012 · Mobile DNA
  81. Patterns of Protein Evolution in Tetrahymena thermophila: Implications for Estimates of Effective Population Size
    Laura A. Katz, Oona Snoeyenbos-West, F. Paul Doerder · 2005 · Molecular Biology and Evolution
  82. The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes
    Marc Tollis, Stéphane Boissinot · 2012 · Genome dynamics
  83. Cut-and-Paste Transposons in Fungi with Diverse Lifestyles
    Anna Muszewska, Kamil Steczkiewicz, Marta M. Stepniewska-Dziubinska, Krzysztof Ginalski · 2017 · Genome Biology and Evolution
  84. The evolution of posttranscriptional regulation
    Bernhard Schaefke, Wei Sun, Yisheng Li, Liang Fang, Wei Chen · 2018 · Wiley Interdisciplinary Reviews - RNA
  85. Experimental evolution reveals hyperparasitic interactions among transposable elements
    Émilie Robillard, Arnaud Le Rouzic, Zheng Zhang, Pierre Capy, Aurélie Hua‐Van · 2016 · Proceedings of the National Academy of Sciences
  86. How Can We Resolve Lewontin’s Paradox?
    B. Charlesworth, J. Jensen · 2022 · Genome Biology and Evolution
  87. A NEW MODEL FOR EXTINCTION AND RECOLONIZATION IN TWO DIMENSIONS: QUANTIFYING PHYLOGEOGRAPHY
    Nick Barton, Jerome Kelleher, Alison M. Etheridge · 2010 · Evolution
  88. Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes
    Sarah Marburger, Markos A. Alexandrou, John Bernard Taggart, Simon Creer, Gary Robert Carvalho, Cláudio Alvarenga de Oliveira, Martin I. Taylor · 2018 · Proceedings of the Royal Society B Biological Sciences
  89. Frequent appearance of novel protein-coding sequences by frameshift translation
    K. Okamura, Lars Feuk, Tomàs Marquès‐Bonet, Arcadi Navarro, Stephen W. Scherer · 2006 · Genomics
  90. Emergence of Switch-Like Behavior in a Large Family of Simple Biochemical Networks
    Dan Siegal‐Gaskins, Maria Katherine Mejía‐Guerra, Gregory D. Smith, Erich Grotewold · 2011 · PLoS Computational Biology
  91. Transposons and non-coding regions drive the intrafamily differences of genome size in insects
    Yuyang Cong, Xinhai Ye, Mei Yang, Kang He, Fei Li · 2022 · iScience
  92. Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life
    Gustavo Caetano‐Anollés, Derek Caetano-Anollés · 2005 · Journal of Molecular Evolution
  93. Genome increase as a clock for the origin and evolution of life.
    Alexei A. Sharov · 2006 · Biology Direct
  94. Extremely Intron-Rich Genes in the Alveolate Ancestors Inferred with a Flexible Maximum-Likelihood Approach
    Miklós Csürös, Igor B. Rogozin, Eugene V. Koonin · 2008 · Molecular Biology and Evolution
  95. Virology: Gulliver among the Lilliputians
    Eugene V. Koonin · 2005 · Current Biology
  96. Structural Organization and Characterization of the Regulatory Element of the Human Carboxylesterase (CES1A1 and CES1A2) genes
    Masakiyo Hosokawa, Tomomi Furihata, Yumiko Yaginuma, Naoko Yamamoto, Natsuko Watanabe, Eiko TSUKADA, Yoshiko OHHATA, Kaoru Kobayashi, Testuo Satoh, Kan Chiba · 2008 · Drug Metabolism and Pharmacokinetics
  97. The Gypsy Database (GyDB) of mobile genetic elements
    Carlos Lloréns, Ricardo Futami, D. Bezemer, Andrés Moyá · 2007 · Nucleic Acids Research
  98. Bdelloid Rotifers: Progress in Understanding the Success of an Evolutionary Scandal
    David B. Mark Welch, Claudia N. Ricci, Matthew S. Meselson · 2009 · Springer eBooks
  99. Genome Size Diversity in Lilium (Liliaceae) Is Correlated with Karyotype and Environmental Traits
    Yunpeng Du, Yu Fang Bi, Mingfang Zhang, Fengping Yang, Guixia Jia, Xiuhai Zhang · 2017 · Frontiers in Plant Science
  100. Applying ecological models to communities of genetic elements: the case of neutral theory
    Stefan Linquist, Karl Cottenie, Tyler A. Elliott, Brent Saylor, Stefan C. Kremer, T. Ryan Gregory · 2015 · Molecular Ecology