Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution

The COG database: an updated version includes eukaryotes

Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410 · see citing works

Genome sequence of the human malaria parasite Plasmodium falciparum

Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., et al. (2002) · Nature · doi:10.1038/nature01097 · Cited by 4,407 · see citing works

A genomic perspective on protein families.

Tatusov, R., Koonin, E., & Lipman, D. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,777 · see citing works

Evidence for a clade of nematodes, arthropods and other moulting animals

Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., & Lake, J. A. (1997) · Nature · doi:10.1038/387489a0 · Cited by 1,609 · see citing works

A kingdom-level phylogeny of eukaryotes based on combined protein data.

Baldauf, S., Roger, A., Wenk-Siefert, I., & Doolittle, W. (2000) · Science · doi:10.1126/science.290.5493.972 · Cited by 1,243 · see citing works

The origin and evolution of model organisms

Hedges, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg929 · Cited by 806 · see citing works

The Exon Theory of GenesPreprint

Gilbert, W. (1987) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1987.052.01.098 · Cited by 393 · see citing works

The recent origins of spliceosomal introns revisited

Logsdon, J. M., Jr. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80031-2 · Cited by 205 · see citing works

Selfish DNA and the origin of introns

Cavalier‐Smith, T. (1985) · Nature · doi:10.1038/315283b0 · Cited by 203 · see citing works

The triosephosphate isomerase gene from maize introns antedate the plant-animal divergence

Marchionni, M. A., & Gilbert, W. (1986) · Cell · doi:10.1016/0092-8674(86)90867-6 · Cited by 189 · see citing works

Large-scale comparison of intron positions among animal, plant, and fungal genes

Fedorov, A. N., Merican, A. F., & Gilbert, W. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242624899 · Cited by 189 · see citing works

Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins

SOUZA, S. J. D., Long, M., Klein, R. J., Roy, S. W., Lin, S., & Gilbert, W. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.5094 · Cited by 183 · see citing works

The evolution of spliceosomal introns

Lynch, M. (2002) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(02)00360-x · Cited by 157 · see citing works

Intron “sliding” and the diversity of intron positions

Stoltzfus, A., Logsdon, J. M., Jr., Palmer, J. D., & Doolittle, W. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.20.10739 · Cited by 156 · see citing works

A spliceosomal intron in Giardia lamblia

Nixon, J. E. J., Wang, A., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B., & Samuelson, J. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.042700299 · Cited by 151 · see citing works

On the ancient nature of introns

Gilbert, W., & Glynias, M. J. (1993) · Gene · doi:10.1016/0378-1119(93)90058-b · Cited by 143 · see citing works

Evolutionary relationships of eukaryotic kingdoms

Kumar, S., & Rzhetsky, A. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02198844 · Cited by 142 · see citing works

Evolution of Intron/Exon Structure of DEAD Helicase Family Genes in Arabidopsis, Caenorhabditis, and DrosophilaPreprint

Boudet, N., Aubourg, S., Toffano‐Nioche, C., Kreis, M. E., & Lecharny, A. (2001) · Genome Research · doi:10.1101/gr.200801 · Cited by 142 · see citing works

Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory.

Logsdon, J. M., Jr., Tyshenko, M. G., Dixon, C. K., D-Jafari, J., Walker, V. K., & Palmer, J. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.18.8507 · Cited by 132 · see citing works

Intron sliding in conserved gene families

Rogozin, I. B., Lyons‐Weiler, J., & Koonin, E. V. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02096-5 · Cited by 118 · see citing works

Molecular evolution: Recent cases of spliceosomal intron gain?

Logsdon, J. M., Stoltzfus, A., & Doolittle, W. F. (1998) · Current Biology · doi:10.1016/s0960-9822(07)00361-2 · Cited by 112 · see citing works

Exon/intron structure of aldehyde dehydrogenase genes supports the “ introns-late ” theory

Rzhetsky, A., Ayala, F. J., Hsu, L. C., Chang, C., & Yoshida, A. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.13.6820 · Cited by 72 · see citing works

Early origin of canonical introns

Simpson, A. G. B., MacQuarrie, E. K., & Roger, A. J. (2002) · Nature · doi:10.1038/419270a · Cited by 60 · see citing works

The Chaperonin Genes of Jakobid and Jakobid-Like Flagellates: Implications for Eukaryotic Evolution

Archibald, J. M., O’Kelly, C. J., & Doolittle, W. F. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004097 · Cited by 59 · see citing works

Testing the “Proto-splice Sites” Model of Intron Origin: Evidence from Analysis of Intron Phase Correlations

Long, M., & Rosenberg, C. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026279 · Cited by 49 · see citing works

Proto-splice site model of intron origin

Dibb, N. J. (1991) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(05)80388-1 · Cited by 42 · see citing works

The Evolution of Single-Copy Drosophila Nuclear 4f-rnp Genes: Spliceosomal Intron Losses Create Polymorphic Alleles

Feiber, A. L., Rangarajan, J. R., & Vaughn, J. C. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-002-2336-y · Cited by 31 · see citing works

Running rings around RNA

Lamond, A. I. (1999) · Nature · doi:10.1038/17697 · Cited by 21 · see citing works

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., et al. (2007) · Science · doi:10.1126/science.1139158 · Cited by 1,555 · see citing works

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works

Alternative splicing and evolution: diversification, exon definition and function

Keren, H., Lev-Maor, G., & Ast, G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2776 · Cited by 1,082 · see citing works

Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae

Carretero‐Paulet, L., Galstyan, A., Roig‐Villanova, I., Martínez‐García, J. F., Bilbao-Castro, J. R., & Robertson, D. L. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.153593 · Cited by 681 · see citing works

The evolution of spliceosomal introns: patterns, puzzles and progress

Roy, S. W., & Gilbert, W. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1807 · Cited by 642 · see citing works

Endosymbiotic theories for eukaryote origin

Martin, W. F., Garg, S., & Zimorski, V. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0330 · Cited by 583 · see citing works

Introns and the origin of nucleus–cytosol compartmentalization

Martin, W. F., & Koonin, E. V. (2006) · Nature · doi:10.1038/nature04531 · Cited by 497 · see citing works

Deep intronic mutations and human disease

Vaz‐Drago, R., Custódio, N., & Carmo‐Fonseca, M. (2017) · Human Genetics · doi:10.1007/s00439-017-1809-4 · Cited by 448 · see citing works

Origin and evolution of spliceosomal introns

Rogozin, I. B., Carmel, L., Csürös, M., & Koonin, E. V. (2012) · Biology Direct · doi:10.1186/1745-6150-7-11 · Cited by 419 · see citing works

The Origins of Eukaryotic Gene Structure

Lynch, M. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj050 · Cited by 391 · see citing works

Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss

Kiontke, K. C., Gavin, N. P., Raynes, Y., Roehrig, C., Piano, F., & Fitch, D. H. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403094101 · Cited by 367 · see citing works

The Function of Introns

Chorev, M., & Carmel, L. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00055 · Cited by 367 · see citing works

Introns: The Functional Benefits of Introns in Genomes

Jo, B.-S., & Choi, S. S. (2015) · Genomics & Informatics · doi:10.5808/gi.2015.13.4.112 · Cited by 357 · see citing works

Intron retention is a major phenomenon in alternative splicing in Arabidopsis

Ner‐Gaon, H., Halachmi, R., Savaldi‐Goldstein, S., Rubin, E., Ophir, R., & Fluhr, R. (2004) · The Plant Journal · doi:10.1111/j.1365-313x.2004.02172.x · Cited by 356 · see citing works

The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?

Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-22 · Cited by 281 · see citing works

Analysis of evolution of exon-intron structure of eukaryotic genes

Rogozin, I. B. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.2.118 · Cited by 268 · see citing works

Vertebrate-Type Intron-Rich Genes in the Marine Annelid <i>Platynereis dumerilii</i>

Raible, F., Tessmar-Raible, K., Osoegawa, K., Wincker, P., Jubin, C., Balavoine, G., Ferrier, D., Benes, V., de Jong, P., Weissenbach, J., et al. (2005) · Science · doi:10.1126/science.1119089 · Cited by 257 · see citing works

Darwinian evolution in the light of genomics

Koonin, E. V. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkp089 · Cited by 254 · see citing works

The biology of intron gain and loss

Jeffares, D. C., Mourier, T., & Penny, D. (2006) · Trends in Genetics · doi:10.1016/j.tig.2005.10.006 · Cited by 296 · see citing works

Molecular evolution of the insect Halloween family of cytochrome P450s: Phylogeny, gene organization and functional conservation

Rewitz, K., O’Connor, M. B., & Gilbert, L. I. (2007) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2007.02.012 · Cited by 234 · see citing works

Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants

Kertész, S., Kerényi, Z., Mérai, Z., Bartos, I., Pálfy, T. B., Barta, E., & Silhavy, D. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl737 · Cited by 231 · see citing works

Patterns of Intron Loss and Gain in Plants: Intron Loss-Dominated Evolution and Genome-Wide Comparison of O. sativa and A. thaliana

Roy, S. W., & Penny, D. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl159 · Cited by 225 · see citing works

The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer

Marabti, E. E., & Younis, I. (2018) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2018.00080 · Cited by 217 · see citing works

Evolution of genome architecture

Koonin, E. V. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.09.015 · Cited by 215 · see citing works

Rates of intron loss and gain: Implications for early eukaryotic evolution

Roy, S. W., & Gilbert, W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500383102 · Cited by 214 · see citing works

Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda

Eyun, S., Soh, H. Y., Posavi, M., Munro, J. B., Hughes, D., Murali, S. C., Qu, J., Dugan, S., Lee, S. L., Chao, H., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx147 · Cited by 205 · see citing works

Origins and Evolution of Spliceosomal Introns

Rodrı́guez-Trelles, F., Tarrı́o, R., & Ayala, F. J. (2006) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.110405.090625 · Cited by 198 · see citing works

Intron gain and loss in segmentally duplicated genes in rice

Lin, H., Zhu, W., da Silva, J. C. F., Gu, X., & Buell, C. R. (2006) · Genome biology · doi:10.1186/gb-2006-7-5-r41 · Cited by 191 · see citing works

Evolutionary Diversity of Vertebrate Small Heat Shock Proteins

Franck, E., Madsen, O., van Rheede, T., Ricard, G., Huynen, M. A., & JONG, W. W. D. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0013-z · Cited by 189 · see citing works

A Toll receptor from Chinese shrimp Fenneropenaeus chinensis is responsive to Vibrio anguillarum infection

YANG, C., Zhang, J., Li, F., Ma, H., ZHANG, Q., Priya, T. A. J., ZHANG, X., & Xiang, J. (2008) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2007.12.012 · Cited by 188 · see citing works

Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica

Jiang, C., Gu, X., & Peterson, T. (2004) · Genome biology · doi:10.1186/gb-2004-5-7-r46 · Cited by 188 · see citing works

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotesPreprint

Schwartz, S., Silva, J., Burstein, D., Pupko, T., Eyras, E., & Ast, G. (2007) · Genome Research · doi:10.1101/gr.6818908 · Cited by 186 · see citing works

Intron Size, Abundance, and Distribution within Untranslated Regions of Genes

Hong, X., Scofield, D. G., & Lynch, M. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl111 · Cited by 184 · see citing works

Systematic analysis of maize class III peroxidase gene family reveals a conserved subfamily involved in abiotic stress response

Wang, Y., Wang, Q., Zhao, Y., Han, G., & Zhu, S. (2015) · Gene · doi:10.1016/j.gene.2015.04.041 · Cited by 182 · see citing works

Three distinct modes of intron dynamics in the evolution of eukaryotesPreprint

Carmel, L., Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2007) · Genome Research · doi:10.1101/gr.6438607 · Cited by 178 · see citing works

The phylogenetic relationships of Caenorhabditis and other rhabditids

Kiontke, K. C. (2005) · WormBook · doi:10.1895/wormbook.1.11.1 · Cited by 170 · see citing works

Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation.

Kondrashov, F. A., Koonin, E. V., Morgunov, I. G., Finogenova, T. V., & Kondrashova, M. N. (2006) · Biology Direct · doi:10.1186/1745-6150-1-31 · Cited by 165 · see citing works

Constraints and plasticity in genome and molecular-phenome evolution

Koonin, E. V., & Wolf, Y. I. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2810 · Cited by 163 · see citing works

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

Csürös, M., Rogozin, I. B., & Koonin, E. V. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002150 · Cited by 163 · see citing works

Prevalence of intron gain over intron loss in the evolution of paralogous gene families

Babenko, V. N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh686 · Cited by 156 · see citing works

Genome-enabled development of DNA markers for ecology, evolution and conservation

Thomson, R. C., Wang, I., & Johnson, J. R. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04650.x · Cited by 148 · see citing works

Origin of Spliceosomal Introns and Alternative SplicingPreprint

Irimia, M., & Roy, S. W. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016071 · Cited by 148 · see citing works

Characterization of intron loss events in mammalsPreprint

Coulombe-Huntington, J., & Majewski, J. (2006) · Genome Research · doi:10.1101/gr.5703406 · Cited by 148 · see citing works

Complex early genes

Roy, S. W., & Gilbert, W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408355101 · Cited by 144 · see citing works

Energetics and genetics across the prokaryote-eukaryote divide

Lane, N. J. (2011) · Biology Direct · doi:10.1186/1745-6150-6-35 · Cited by 142 · see citing works

Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle, Tribolium castaneum

Zhu, F., Moural, T. W., Shah, K., & Palli, S. R. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-174 · Cited by 137 · see citing works

Comparative genomic analysis of fungal genomes reveals intron-rich ancestors

Stajich, J., Dietrich, F. S., & Roy, S. W. (2007) · Genome biology · doi:10.1186/gb-2007-8-10-r223 · Cited by 133 · see citing works

Patterns of Intron Gain and Loss in Fungi

Nielsen, C. B., Friedman, B. A., Birren, B. W., Burge, C. B., & Galagan, J. E. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020422 · Cited by 128 · see citing works

Origins of recently gained introns in Caenorhabditis

Coghlan, A., & Wolfe, K. H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308192101 · Cited by 128 · see citing works

Evolution of secretin family GPCR members in the metazoa

Cardoso, J. C. R., Pinto, V., Vieira, F. A., Clark, M. S., & Power, D. M. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-108 · Cited by 123 · see citing works

Extensive, Recent Intron Gains in Daphnia Populations

Li, W., Tucker, A. E., Sung, W., Thomas, W. K., & Lynch, M. (2009) · Science · doi:10.1126/science.1179302 · Cited by 122 · see citing works

The pattern of intron loss

Roy, S. W., & Gilbert, W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408274102 · Cited by 121 · see citing works

Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri)

Cao, Y., Han, Y., Meng, D., Li, D., Jin, Q., Lin, Y., & Cai, Y. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01874 · Cited by 120 · see citing works

Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

Li, W., Liu, B., Yu, L., Feng, D., Wang, H., & Wang, J. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-90 · Cited by 120 · see citing works

Evolution of the Caenorhabditis elegans Genome

Cutter, A. D., Dey, A., & Murray, R. L. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp048 · Cited by 120 · see citing works

Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications

Leterrier, M., Holappa, L. D., Broglie, K. E., & Beckles, D. M. (2008) · BMC Plant Biology · doi:10.1186/1471-2229-8-98 · Cited by 118 · see citing works

Coevolution of genomic intron number and splice sites

Irimia, M., Penny, D., & Roy, S. W. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.04.001 · Cited by 108 · see citing works

Genome-wide analysis of cytochrome P450 monooxygenase genes in the silkworm, Bombyx mori

Ai, J., Zhu, Y., Duan, J., Yu, Q., Zhang, G., Fei, W., & Xiang, Z. (2011) · Gene · doi:10.1016/j.gene.2011.03.002 · Cited by 107 · see citing works

Evolutionary convergence of alternative splicing in ion channels

Copley, R. R. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.02.001 · Cited by 106 · see citing works

Spliceosomal introns as tools for genomic and evolutionary analysis

Irimia, M., & Roy, S. W. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn012 · Cited by 102 · see citing works

Conservation versus parallel gains in intron evolution

Sverdlov, A. V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki316 · Cited by 101 · see citing works

A Very High Fraction of Unique Intron Positions in the Intron-Rich Diatom Thalassiosira pseudonana Indicates Widespread Intron Gain

Roy, S. W., & Penny, D. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm048 · Cited by 101 · see citing works

Do transposable elements really contribute to proteomes?

Gotea, V., & Makałowski, W. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.03.006 · Cited by 97 · see citing works

The C. elegans Rab Family: Identification, Classification and Toolkit Construction

Gallegos, M. E., Balakrishnan, S., Chandramouli, P., Arora, S., Azameera, A., Babushekar, A., Bargoma, E., Bokhari, A. A., Chava, S. K., Das, P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049387 · Cited by 90 · see citing works

Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis

Vaňáčová, Š., Yan, W., Carlton, J. M., & Johnson, P. J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407500102 · Cited by 90 · see citing works

Wagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos

Alekseyenko, A. V., Lee, C. J., & Suchard, M. A. (2008) · Systematic Biology · doi:10.1080/10635150802434394 · Cited by 89 · see citing works

Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes

Rogozin, I. B., Basu, M. K., Csürös, M., & Koonin, E. V. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp011 · Cited by 88 · see citing works

Evolutionarily conserved genes preferentially accumulate intronsPreprint

Carmel, L., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2007) · Genome Research · doi:10.1101/gr.5978207 · Cited by 87 · see citing works

Identifying the mechanisms of intron gain: progress and trends

Yenerall, P. M., & Zhou, L. (2012) · Biology Direct · doi:10.1186/1745-6150-7-29 · Cited by 86 · see citing works

Genome-wide functional analysis of human 5' untranslated region introns

Cenik, C., Derti, A., Mellor, J. C., Berriz, G. F., & Roth, F. P. (2010) · Genome biology · doi:10.1186/gb-2010-11-3-r29 · Cited by 84 · see citing works

New Maximum Likelihood Estimators for Eukaryotic Intron Evolution

Nguyen, H. D., Yoshihama, M., & Kenmochi, N. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0010079 · Cited by 82 · see citing works

Plant Spliceosomal Introns: Not Only Cut and Paste

Morello, L., & Breviario, D. (2008) · Current Genomics · doi:10.2174/138920208784533629 · Cited by 81 · see citing works

Intron Loss and Gain in Drosophila

Coulombe‐Huntington, J., & Majewski, J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm235 · Cited by 81 · see citing works

Feminized tassels of maize mop1 and ts1 mutants exhibit altered levels of miR156 and specific SBP-box genes

Hultquist, J. F., & Dorweiler, J. E. (2008) · Planta · doi:10.1007/s00425-008-0813-2 · Cited by 80 · see citing works

Intron-Dominated Genomes of Early Ancestors of Eukaryotes

Koonin, E. V. (2009) · Journal of Heredity · doi:10.1093/jhered/esp056 · Cited by 80 · see citing works

Patterns of intron gain and conservation in eukaryotic genes

Carmel, L., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-192 · Cited by 80 · see citing works

Rel homology domain-containing transcription factors in the cnidarian Nematostella vectensis

Sullivan, J. C., Kalaitzidis, D., Gilmore, T. D., & Finnerty, J. R. (2006) · Development Genes and Evolution · doi:10.1007/s00427-006-0111-6 · Cited by 79 · see citing works

Identification of mammalian orthologs using local synteny

Jun, J., Mandoiu, I. I., & Nelson, C. E. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-630 · Cited by 78 · see citing works

Evolution of the Metazoan-Specific Importin α Gene Family

Mason, D. A., Stage, D. E., & Goldfarb, D. S. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9215-8 · Cited by 77 · see citing works

Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor

Garg, S. G., & Martin, W. F. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw136 · Cited by 76 · see citing works

Preferential loss and gain of introns in 3′ portions of genes suggests a reverse-transcription mechanism of intron insertion

Sverdlov, A. V., Babenko, V. N., Rogozin, I. B., & Koonin, E. V. (2004) · Gene · doi:10.1016/j.gene.2004.05.027 · Cited by 76 · see citing works

Genomewide identification, classification and analysis of NAC type gene family in maize

Peng, X., Zhao, Y., Li, X., WU, M., CHAI, W., SHENG, L., Wang, Y., Dong, Q., Jiang, H., & Cheng, B. (2015) · Journal of Genetics · doi:10.1007/s12041-015-0526-9 · Cited by 76 · see citing works

CRISPR/Cas9-mediated mutagenesis in the sea lamprey, Petromyzon marinus: a powerful tool for understanding ancestral gene functions in vertebrates

Square, T. A., Romášek, M., Jandzík, D., Cattell, M. V., Klymkowsky, M. W., & Medeiros, D. M. (2015) · Development · doi:10.1242/dev.125609 · Cited by 74 · see citing works

Plant Actin-Depolymerizing Factors Possess Opposing Biochemical Properties Arising from Key Amino Acid Changes throughout Evolution

Nan, Q., Qian, D., Niu, Y., He, Y., Tong, S., Niu, Z., Ma, J., Yang, Y., An, L., Wan, D., et al. (2017) · The Plant Cell · doi:10.1105/tpc.16.00690 · Cited by 74 · see citing works

The Peculiarities of Large Intron Splicing in Animals

Shepard, S. S., McCreary, M., & Fedorov, A. N. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007853 · Cited by 73 · see citing works

A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes

Chernikova, D., Motamedi, S., Csürös, M., Koonin, E. V., & Rogozin, I. B. (2011) · Biology Direct · doi:10.1186/1745-6150-6-26 · Cited by 72 · see citing works

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

Awan, A. R., Manfredo, A., & Pleiss, J. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218353110 · Cited by 72 · see citing works

Support for the Coelomata Clade of Animals from a Rigorous Analysis of the Pattern of Intron Conservation

Zheng, J., Rogozin, I. B., Koonin, E. V., & Przytycka, T. M. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm207 · Cited by 70 · see citing works

The landscape of human mutually exclusive splicing

Hatje, K., Rahman, R., Vidal, R. O., Simm, D., Hammesfahr, B., Bansal, V., Rajput, A., Mickael, M., Sun, T., Bonn, S., et al. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177728 · Cited by 70 · see citing works

Mystery of intron gain: new data and new models

Roy, S. W., & Irimia, M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.11.004 · Cited by 69 · see citing works

High Rate of Recent Intron Gain and Loss in Simultaneously Duplicated Arabidopsis Genes

Knowles, D. G., & McLysaght, A. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl017 · Cited by 68 · see citing works

Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements

Rogozin, I. B., Wolf, Y. I., Carmel, L., & Koonin, E. V. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm029 · Cited by 68 · see citing works

PIECE: a database for plant gene structure comparison and evolution

Wang, Y., You, F. M., Lazo, G. R., Luo, M., Thilmony, R. L., Gordon, S., Kianian, S. F., & Gu, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1109 · Cited by 67 · see citing works

Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron numberPreprint

Roy, S. W., & Hartl, D. L. (2006) · Genome Research · doi:10.1101/gr.4845406 · Cited by 67 · see citing works

Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae

Lin, X., Zhang, Y., Kuang, H., & Chen, J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-335 · Cited by 66 · see citing works

Duplication and Functional Diversification of HAP3 Genes Leading to the Origin of the Seed-Developmental Regulatory Gene, LEAFY COTYLEDON1 (LEC1), in Nonseed Plant Genomes

Xie, Z., Li, X., Glover, B. J., Bai, S., Rao, G., Luo, J., & Yang, J. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn105 · Cited by 66 · see citing works

Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Pucker, B., & Brockington, S. F. (2018) · BMC Genomics · doi:10.1186/s12864-018-5360-z · Cited by 65 · see citing works

Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Aleem, M., Riaz, A., Raza, Q. S., Aleem, M., Aslam, M., Kong, K., Atif, R. M., Kashif, M., Bhat, J. A., & Zhao, T. (2021) · Genomics · doi:10.1016/j.ygeno.2021.11.016 · Cited by 65 · see citing works

Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis

Irimia, M., Rukov, J. L., Penny, D., García‐Fernàndez, J., Vinther, J., & Roy, S. W. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm262 · Cited by 65 · see citing works

Comparative Analysis of Bacterial-Origin Genes for Plant Mitochondrial Ribosomal Proteins

Bonen, L., & Calixte, S. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj080 · Cited by 65 · see citing works

Analysis of evolution of exon-intron structure of eukaryotic genes

Rogozin, I. B. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.2.118 · Cited by 268 · see citing works

Protein‐Coding Segments: Evolution of Exon–Intron Gene Structure

Igor, R. E. (2021) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0029344

Patterns of intron gain and conservation in eukaryotic genes

Carmel, L., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-192 · Cited by 80 · see citing works

Spliceosomal Introns: New Insights into their Evolution

Zhaxybayeva, O., & Gogarten, J. P. (2003) · Current Biology · doi:10.1016/j.cub.2003.09.017 · Cited by 33 · see citing works

Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolutionPreprint

Roy, S. W., & Penny, D. (2006) · Genome Research · doi:10.1101/gr.5410606 · Cited by 44 · see citing works