Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
Open accessAbstract
This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length >100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a “syntenic” subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that ≈2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments.
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Comparing induced pairwise human-dog alignments to direct pairwise alignments computed using the chains and nets pipeline, the same level of Jaccard similarity was found for both high- and low-quality assembly alignments.
“Reinforcing this, comparing the induced pairwise alignments of human–dog to direct pairwise alignments computed using the established chains and nets pipeline30, we find the same level of Jaccard similarity for both the high- and low-quality assembly alignments (Supplementary Fig. 5).”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [30]
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The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400 · see citing works
Self-citationTandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works
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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 4,408 · see citing works
Self-citationA gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475 · see citing works
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750 · see citing works
Initial sequence of the chimpanzee genome and comparison with the human genome
The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459 · see citing works
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods · doi:10.1038/nmeth.2148 · Cited by 1,423 · see citing works
Evolutionary and biomedical insights from the rhesus macaque genome.
Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science · doi:10.1126/science.1139247 · Cited by 1,403 · see citing works
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Assessing the evolutionary impact of amino acid mutations in the human genome.
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000083 · Cited by 628 · see citing works
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Pollen, A. A., Bhaduri, A., Andrews, M. G., Nowakowski, T. J., Meyerson, O. S., Mostajo-Radji, M. A., Di Lullo, E., Alvarado, B., Bedolli, M., Dougherty, M. L., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.017 · Cited by 600 · see citing works
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Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586 · see citing works
Self-citationPatterns of Positive Selection in Six Mammalian Genomes
Kosiol, C., Vinař, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., & Siepel, A. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000144 · Cited by 576 · see citing works
Widespread Genomic Signatures of Natural Selection in Hominid Evolution
McVicker, G., Gordon, D., Davis, C., & Green, P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000471 · Cited by 456 · see citing works
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
Whalen, S., Truty, R. M., & Pollard, K. S. (2016) · Nature Genetics · doi:10.1038/ng.3539 · Cited by 456 · see citing works
Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Ann Blomberg, L., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000475 · Cited by 416 · see citing works
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Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., et al. (2023) · Science · doi:10.1126/science.abn3107 · Cited by 209 · see citing works
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Computational challenges in the analysis of ancient DNA
Prüfer, K., Stenzel, U., Hofreiter, M., Pääbo, S., Kelso, J., & Green, R. E. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r47 · Cited by 155 · see citing works
“The location of the human and chimp hits for each read is verified by using liftover [50] to map the coordinates of the human hit to the chimpanzee genome and the coordinate of the chimpanzee hit to the human genome.”
BackgroundMethodBourque, G., Zdobnov, E. M., Bork, P., Pevzner, P. A., & Tesler, G. (2005) · Genome Research · doi:10.1101/gr.3002305 · Cited by 162 · see citing works
Manrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., et al. (2021) · Physics of Life Reviews · doi:10.1016/j.plrev.2021.03.004 · Cited by 88 · see citing works
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Aloni, R., Olender, T., & Lancet, D. (2006) · Genome Biology · doi:10.1186/gb-2006-7-10-r88 · Cited by 56 · see citing works
Krasheninnikova, K., Diekhans, M., Armstrong, J., Dievskii, A., Paten, B., & O'Brien, S. (2020) · GigaScience · doi:10.1093/gigascience/giaa047 · Cited by 30 · see citing works
Wang, Z., & Zhang, Q. (2009) · Evolutionary Bioinformatics · doi:10.4137/ebo.s2948 · Cited by 16 · see citing works
- Authors
- Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D.
- Affiliations
- Pennsylvania State University (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2003-09-19
- Volume
- 100
- Issue
- 20
- Pages
- 11484-11489
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC208784
- OpenAlex
- W2122598328
- Cited by
- 850
- References
- 2
- Citations by year
- 2026: 25 · 2025: 31 · 2024: 48 · 2023: 33 · 2022: 27 · 2021: 33 · 2020: 37 · 2019: 36 · 2018: 50 · 2017: 25 · 2016: 30 · 2015: 37 · 2014: 38 · 2013: 33 · 2012: 36
- FWCI
- 18.70
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (HG 02238, P41HG002371, R01HG002238)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- genomic duplication, genomic deletions, chromosomal rearrangements, inversion, transposition, synteny, pseudogenes, gene loss
- MeSH terms
- Animals, Genome, Gene Deletion, Evolution, Molecular, Gene Duplication, Mice
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