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For: Martin KJ, Holland PWH. Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication. Mol Biol Evol 2014;31:2592-611. [PMID: 24974377 PMCID: PMC4166920 DOI: 10.1093/molbev/msu202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2014] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Tian Z, Wei M, Xue R, Song L, Li H, Ji H, Xiao P, Sun J. Comparative study on the transcriptional activities of grass carp (Ctenopharyngodon idellus) peroxisome proliferator-activated receptors induced by different fatty acids. Comp Biochem Physiol B Biochem Mol Biol 2024;275:111021. [PMID: 39151662 DOI: 10.1016/j.cbpb.2024.111021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
2
Wang B, Wu B, Liu X, Hu Y, Ming Y, Bai M, Liu J, Xiao K, Zeng Q, Yang J, Wang H, Guo B, Tan C, Hu Z, Zhao X, Li Y, Yue Z, Mei J, Jiang W, Yang Y, Li Z, Gao Y, Chen L, Jian J, Du H. Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzad002. [PMID: 38862424 DOI: 10.1093/gpbjnl/qzad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 06/13/2024]
3
Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nat Ecol Evol 2024;8:519-535. [PMID: 38216617 DOI: 10.1038/s41559-023-02299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024]
4
Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Nature 2024;627:811-820. [PMID: 38262590 PMCID: PMC10972751 DOI: 10.1038/s41586-024-07070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
5
Redmond AK, Casey D, Gundappa MK, Macqueen DJ, McLysaght A. Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor. Nat Commun 2023;14:2879. [PMID: 37208359 DOI: 10.1038/s41467-023-38714-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/12/2023] [Indexed: 05/21/2023]  Open
6
Zhang J. What Has Genomics Taught An Evolutionary Biologist? GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:1-12. [PMID: 36720382 PMCID: PMC10373158 DOI: 10.1016/j.gpb.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
7
Mulhair PO, Crowley L, Boyes DH, Harper A, Lewis OT, Holland PW. Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera. Genome Res 2023;33:32-44. [PMID: 36617663 PMCID: PMC9977156 DOI: 10.1101/gr.277118.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
8
Mendizábal-Castillero M, Merlo MA, Cross I, Rodríguez ME, Rebordinos L. Genomic Characterization of hox Genes in Senegalese Sole (Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes. Animals (Basel) 2022;12:ani12243586. [PMID: 36552509 PMCID: PMC9774920 DOI: 10.3390/ani12243586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]  Open
9
Parey E, Louis A, Montfort J, Guiguen Y, Crollius HR, Berthelot C. An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication. Genome Res 2022;32:1685-1697. [PMID: 35961774 PMCID: PMC9528989 DOI: 10.1101/gr.276953.122] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
10
Torres-Aguila NP, Salonna M, Hoppler S, Ferrier DEK. Evolutionary diversification of the canonical Wnt signaling effector TCF/LEF in chordates. Dev Growth Differ 2022;64:120-137. [PMID: 35048372 PMCID: PMC9303524 DOI: 10.1111/dgd.12771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/29/2022]
11
Gundappa MK, To TH, Grønvold L, Martin SAM, Lien S, Geist J, Hazlerigg D, Sandve SR, Macqueen DJ. Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution. Mol Biol Evol 2022;39:msab310. [PMID: 34718723 PMCID: PMC8760942 DOI: 10.1093/molbev/msab310] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
12
Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nat Commun 2021;12:4489. [PMID: 34301952 PMCID: PMC8302630 DOI: 10.1038/s41467-021-24573-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/25/2021] [Indexed: 02/07/2023]  Open
13
Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
14
Bayramov AV, Ermakova GV, Kuchryavyy AV, Zaraisky AG. Genome Duplications as the Basis of Vertebrates’ Evolutionary Success. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
15
Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol 2020;4:820-830. [PMID: 32313176 PMCID: PMC7269912 DOI: 10.1038/s41559-020-1156-z] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/19/2020] [Indexed: 01/24/2023]
16
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 2020;4:841-852. [PMID: 32231327 PMCID: PMC7269910 DOI: 10.1038/s41559-020-1166-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
17
Liu DW, Wang FY, Lin JJ, Thompson A, Lu Y, Vo D, Yan HY, Zakon H. The Cone Opsin Repertoire of Osteoglossomorph Fishes: Gene Loss in Mormyrid Electric Fish and a Long Wavelength-Sensitive Cone Opsin That Survived 3R. Mol Biol Evol 2019;36:447-457. [PMID: 30590689 DOI: 10.1093/molbev/msy241] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
18
De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. PLoS One 2019;14:e0218085. [PMID: 31188893 PMCID: PMC6561569 DOI: 10.1371/journal.pone.0218085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/25/2019] [Indexed: 12/18/2022]  Open
19
Houston RD, Macqueen DJ. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet 2019;50:3-14. [PMID: 30426521 PMCID: PMC6492011 DOI: 10.1111/age.12748] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
20
Kavouras M, Malandrakis EE, Golomazou E, Konstantinidis I, Blom E, Palstra AP, Anastassiadis K, Panagiotaki P, Exadactylos A. Hox gene expression profiles during embryonic development of common sole. ANIM BIOL 2019. [DOI: 10.1163/15707563-17000123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
21
Clark JW, Donoghue PCJ. Whole-Genome Duplication and Plant Macroevolution. TRENDS IN PLANT SCIENCE 2018;23:933-945. [PMID: 30122372 DOI: 10.1016/j.tplants.2018.07.006] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/29/2018] [Accepted: 07/12/2018] [Indexed: 05/18/2023]
22
Pascual-Anaya J, Sato I, Sugahara F, Higuchi S, Paps J, Ren Y, Takagi W, Ruiz-Villalba A, Ota KG, Wang W, Kuratani S. Hagfish and lamprey Hox genes reveal conservation of temporal colinearity in vertebrates. Nat Ecol Evol 2018;2:859-866. [PMID: 29610468 DOI: 10.1038/s41559-018-0526-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/01/2018] [Indexed: 11/09/2022]
23
Gallagher MD, Macqueen DJ. Evolution and Expression of Tissue Globins in Ray-Finned Fishes. Genome Biol Evol 2018;9:32-47. [PMID: 28173090 PMCID: PMC5381549 DOI: 10.1093/gbe/evw266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/30/2022]  Open
24
MacKintosh C, Ferrier DEK. Recent advances in understanding the roles of whole genome duplications in evolution. F1000Res 2017;6:1623. [PMID: 28928963 PMCID: PMC5590085 DOI: 10.12688/f1000research.11792.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2018] [Indexed: 01/21/2023]  Open
25
Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol 2017;18:111. [PMID: 28615063 PMCID: PMC5470254 DOI: 10.1186/s13059-017-1241-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/19/2017] [Indexed: 12/26/2022]  Open
26
Complex Genes Are Preferentially Retained After Whole-Genome Duplication in Teleost Fish. J Mol Evol 2017;84:253-258. [PMID: 28492966 DOI: 10.1007/s00239-017-9794-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/03/2017] [Indexed: 11/27/2022]
27
Martin KJ, Holland PWH. Diversification of Hox Gene Clusters in Osteoglossomorph Fish in Comparison to Other Teleosts and the Spotted Gar Outgroup. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017;328:638-644. [DOI: 10.1002/jez.b.22726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/14/2016] [Accepted: 12/25/2016] [Indexed: 11/06/2022]
28
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Sci Rep 2016;6:24501. [PMID: 27089831 PMCID: PMC4835728 DOI: 10.1038/srep24501] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/30/2016] [Indexed: 11/09/2022]  Open
29
Zwarycz AS, Nossa CW, Putnam NH, Ryan JF. Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the EarthwormEisenia fetida. Genome Biol Evol 2016. [DOI: 10.1093/gbe/evv243 v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
30
Zwarycz AS, Nossa CW, Putnam NH, Ryan JF. Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida. Genome Biol Evol 2015;8:271-81. [PMID: 26659921 PMCID: PMC4758240 DOI: 10.1093/gbe/evv243] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2015] [Indexed: 11/14/2022]  Open
31
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. Proc Natl Acad Sci U S A 2015;112:14918-23. [PMID: 26578810 DOI: 10.1073/pnas.1507669112] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
32
Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015;125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
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