The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Open accessAbstract
Ingo Braasch, John Postlethwait and colleagues report the genome of the spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before genome duplication. Their data provide insights into the evolution of genes involved in immunity, mineralization and development and facilitate the comparison of cis-regulatory elements between teleosts and humans. To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
Woolfe, A., Goodson, M., Goode, D. K., Snell, P., McEwen, G. K., Vavouri, T., Smith, S. F., North, P., Callaway, H., Kelly, K., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030007 · Cited by 970
Lartillot, N., Rodrigue, N., Stubbs, D., & Richer, J. (2013) · Systematic Biology · doi:10.1093/sysbio/syt022 · Cited by 871
Cited by
Deeply conserved synteny resolves early events in vertebrate evolution
Simakov, O., Marlétaz, F., Yue, J.-X., O’Connell, B., Jenkins, J., Brandt, A., Calef, R., Tung, C.-H., Huang, T.-K., Schmutz, J., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1156-z · Cited by 363
Genetic load: genomic estimates and applications in non-model animals
Bertorelle, G., Raffini, F., Bosse, M., Bortoluzzi, C., Iannucci, A., Trucchi, E., Morales, H. E., & van Oosterhout, C. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00448-x · Cited by 306
Smith, J. J., Timoshevskaya, N., Ye, C., Holt, C., Keinath, M. C., Parker, H. J., Cook, M. E., Hess, J. E., Narum, S. R., Lamanna, F., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0036-1 · Cited by 305
Self-citationEvolution and Diversity of Transposable Elements in Vertebrate Genomes
Sotero-Caio, C. G., Platt, R. N., Suh, A., & Ray, D. A. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evw264 · Cited by 283
Kelmer Sacramento, E., Kirkpatrick, J. M., Mazzetto, M., Baumgart, M., Bartolome, A., Di Sanzo, S., Caterino, C., Sanguanini, M., Papaevgeniou, N., Lefaki, M., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209596 · Cited by 236
Deeply conserved synteny and the evolution of metazoan chromosomes
Simakov, O., Bredeson, J., Berkoff, K., Marletaz, F., Mitros, T., Schultz, D. T., O’Connell, B. L., Dear, P., Martinez, D. E., Steele, R. E., et al. (2022) · Science Advances · doi:10.1126/sciadv.abi5884 · Cited by 197
Giant lungfish genome elucidates the conquest of land by vertebrates
Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J. M., Irisarri, I., Wong, W. Y., Nowoshilow, S., Kneitz, S., Kawaguchi, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03198-8 · Cited by 211
Self-citationChromosome evolution at the origin of the ancestral vertebrate genome
Sacerdot, C., Louis, A., Bon, C., Berthelot, C., & Roest Crollius, H. (2018) · Genome Biology · doi:10.1186/s13059-018-1559-1 · Cited by 206
African lungfish genome sheds light on the vertebrate water-to-land transition
Wang, K., Wang, J., Zhu, C., Yang, L., Ren, Y., Ruan, J., Fan, G., Hu, J., Xu, W., Bi, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.047 · Cited by 192
Fish pigmentation and the melanocortin system
Cal, L., Suarez-Bregua, P., Cerdá-Reverter, J. M., Braasch, I., & Rotllant, J. (2017) · Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology · doi:10.1016/j.cbpa.2017.06.001 · Cited by 159
Self-citationNakatani, Y., Shingate, P., Ravi, V., Pillai, N. E., Prasad, A., McLysaght, A., & Venkatesh, B. (2021) · Nature Communications · doi:10.1038/s41467-021-24573-z · Cited by 151
Self-citationTracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes
Bi, X., Wang, K., Yang, L., Pan, H., Jiang, H., Wei, Q., Fang, M., Yu, H., Zhu, C., Cai, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.046 · Cited by 145
Diversity as opportunity: Insights from 600 million years of AHR evolution
Hahn, M. E., Karchner, S. I., & Merson, R. R. (2017) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2017.02.003 · Cited by 134
Phylogenetic classification of living and fossil ray-finned fishes (Actinopterygii)
Near, T. J., & Thacker, C. E. (2024) · Bulletin of the Peabody Museum of Natural History · doi:10.3374/014.065.0101 · Cited by 124
Topological structures and syntenic conservation in sea anemone genomes
Zimmermann, B., Montenegro, J. D., Robb, S. M. C., Fropf, W. J., Weilguny, L., He, S., Chen, S., Lovegrove-Walsh, J., Hill, E. M., Chen, C.-Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44080-7 · Cited by 106
The emerging phylogenetic perspective on the evolution of actinopterygian fishes
Dornburg, A., & Near, T. J. (2021) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-122120-122554 · Cited by 95
Parey, E., Louis, A., Montfort, J., Guiguen, Y., Crollius, H. R., & Berthelot, C. (2022) · Genome Research · doi:10.1101/gr.276953.122 · Cited by 83
Self-citationGranneman, J. G., Kimler, V. A., Zhang, H., Ye, X., Luo, X., Postlethwait, J. H., & Thummel, R. (2017) · eLife · doi:10.7554/elife.21771 · Cited by 77
Self-citationEvolution of the Chordate Telencephalon
Briscoe, S. D., & Ragsdale, C. W. (2019) · Current Biology · doi:10.1016/j.cub.2019.05.026 · Cited by 75
Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes
Spiewak, J. E., Bain, E. J., Liu, J., Kou, K., Sturiale, S. L., Patterson, L. B., Diba, P., Eisen, J. S., Braasch, I., Ganz, J., et al. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007538 · Cited by 58
Self-citationZebrafish models of sarcopenia
Daya, A., Donaka, R., & Karasik, D. (2020) · Disease Models & Mechanisms · doi:10.1242/dmm.042689 · Cited by 55
Yuan, X., Song, M., Devine, P., Bruneau, B. G., Scott, I. C., & Wilson, M. D. (2018) · Nature Communications · doi:10.1038/s41467-018-07451-z · Cited by 51
Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications
Parey, E., Louis, A., Cabau, C., Guiguen, Y., Roest Crollius, H., & Berthelot, C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa149 · Cited by 49
Self-citationTørresen, O. K., Brieuc, M. S. O., Solbakken, M. H., Sørhus, E., Nederbragt, A. J., Jakobsen, K. S., Meier, S., Edvardsen, R. B., & Jentoft, S. (2018) · BMC Genomics · doi:10.1186/s12864-018-4616-y · Cited by 46
The lasting after-effects of an ancient polyploidy on the genomes of teleosts
Conant, G. C. (2020) · PLOS ONE · doi:10.1371/journal.pone.0231356 · Cited by 42
Sequencing and chromosome-scale assembly of the giant Pleurodeles waltl genome
Brown, T., Elewa, A., Iarovenko, S., Subramanian, E., Araus, A. J., Petzold, A., Suzuki, M., Suzuki, K.-I. T., Hayashi, T., Toyoda, A., et al. (2022) · doi:10.1101/2022.10.19.512763 · Cited by 37
Nakatani, Y., & McLysaght, A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx259 · Cited by 35
Aman, A. J., Saunders, L. M., Carr, A. A., Srivatasan, S., Eberhard, C., Carrington, B., Watkins-Chow, D., Pavan, W. J., Trapnell, C., & Parichy, D. M. (2023) · eLife · doi:10.7554/elife.86670 · Cited by 30
Rozenfeld, C., Blanca, J., Gallego, V., García-Carpintero, V., Herranz-Jusdado, J. G., Pérez, L., Asturiano, J. F., Cañizares, J., & Peñaranda, D. S. (2019) · PLOS ONE · doi:10.1371/journal.pone.0218085 · Cited by 28
Dornburg, A., Wcisel, D. J., Zapfe, K., Ferraro, E., Roupe-Abrams, L., Thompson, A. W., Braasch, I., Ota, T., & Yoder, J. A. (2021) · Immunogenetics · doi:10.1007/s00251-021-01225-6 · Cited by 16
Self-citationRao, A., Lyu, B., Jahan, I., Lubertozzi, A., Zhou, G., Tedeschi, F., Jankowsky, E., Kang, J., Carstens, B., Poss, K. D., et al. (2023) · Development · doi:10.1242/dev.201376 · Cited by 13
Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes
Liu, K., Wang, Q., Wang, N., Meng, L., Li, S., Wang, H., Liu, Y., Liu, Q., Zhang, Y., Doretto, L. B., et al. (2025) · Advanced Science · doi:10.1002/advs.202417251 · Cited by 3
Self-citationZebrafish relatives as models for functional comparative genetics and genomics
Podobnik, M., Lu, Y., Irion, U., & Currie, P. D. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-01007-4 · Cited by 1
Johal, S., Elsayed, R., Wang, D., Talbot, C. D., Feuda, R., Panfilio, K. A., & Nelson, A. C. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf213 · Cited by 1
Metadata
- Authors
- Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A. M., Campbell, M. S., Barrell, D., Martin, K. J., Mulley, J. F., Ravi, V., Lee, A. P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F. E. G., Sun, Y., Hertel, J., Beam, M. J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J. H., Litman, G. W., Litman, R. T., Mikami, M., Ota, T., Saha, N. R., Williams, L., Stadler, P. F., Wang, H., Taylor, J. S., Fontenot, Q., Ferrara, A., Searle, S. M. J., Aken, B., Yandell, M., Schneider, I., Yoder, J. A., Volff, J.-N., Meyer, A., Amemiya, C. T., Venkatesh, B., Holland, P. W. H., Guiguen, Y., Bobe, J., Shubin, N. H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., & Postlethwait, J. H.
- Venue
- Nature Genetics
- Published
- 2016-03-07
- Volume
- 48
- Issue
- 4
- Pages
- 427-437
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2296550515
- Cited by
- 618
- References
- 13
- FWCI
- 86.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
