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For: Chalopin D, Naville M, Plard F, Galiana D, Volff JN. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 2015;7:567-80. [PMID: 25577199 PMCID: PMC4350176 DOI: 10.1093/gbe/evv005] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
Number Cited by Other Article(s)
1
do Nascimento Moreira C, Crampton WGR, de Andrade Affonso PH, Martins C, Cardoso AL. Genomic landscape of repetitive DNAs in Neotropical electric fishes. Mol Genet Genomics 2025;300:40. [PMID: 40186627 DOI: 10.1007/s00438-025-02248-4] [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: 10/28/2024] [Accepted: 03/21/2025] [Indexed: 04/07/2025]
2
de Oliveira FS, Brann T, Wolf IR, Nogaroto V, Martins C, Protasio AV, Vicari MR. The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae). Chromosome Res 2025;33:6. [PMID: 40186682 DOI: 10.1007/s10577-025-09765-3] [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: 12/19/2024] [Revised: 03/07/2025] [Accepted: 03/17/2025] [Indexed: 04/07/2025]
3
Ancona L, Nitta Fernandes FA, Biello R, Chiocchio A, Castrignanò T, Barucca M, Canestrelli D, Trucchi E. Evolutionary Dynamics of Transposable Element Activity and Regulation in the Apennine Yellow-Bellied Toad (Bombina pachypus). Genome Biol Evol 2025;17:evaf062. [PMID: 40211594 PMCID: PMC12008745 DOI: 10.1093/gbe/evaf062] [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] [Accepted: 03/27/2025] [Indexed: 04/20/2025]  Open
4
Petroll R, Papareddy RK, Krela R, Laigle A, Rivière Q, Bišova K, Mozgová I, Borg M. The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants. Mol Biol Evol 2025;42:msaf064. [PMID: 40127687 PMCID: PMC11982613 DOI: 10.1093/molbev/msaf064] [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: 09/23/2024] [Revised: 02/26/2025] [Accepted: 03/05/2025] [Indexed: 03/26/2025]  Open
5
Varga Z, Kagan F, Maegawa S, Nagy Á, Okendo J, Burgess SM, Weinberg ES, Varga M. Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.28.640854. [PMID: 40093107 PMCID: PMC11908130 DOI: 10.1101/2025.02.28.640854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
6
Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. Genome Biol 2025;26:14. [PMID: 39844208 PMCID: PMC11753138 DOI: 10.1186/s13059-025-03475-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 01/06/2025] [Indexed: 01/24/2025]  Open
7
Mallik R, Wcisel DJ, Near TJ, Yoder JA, Dornburg A. Investigating the Impact of Whole-Genome Duplication on Transposable Element Evolution in Teleost Fishes. Genome Biol Evol 2025;17:evae272. [PMID: 39715451 PMCID: PMC11785729 DOI: 10.1093/gbe/evae272] [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: 04/18/2024] [Revised: 12/08/2024] [Accepted: 12/13/2024] [Indexed: 12/25/2024]  Open
8
Zhao J, Xie L, Zhao X, Li L, Cui J, Chen J. Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae). G3 (BETHESDA, MD.) 2024;14:jkae223. [PMID: 39290157 PMCID: PMC11540328 DOI: 10.1093/g3journal/jkae223] [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: 05/28/2024] [Revised: 08/27/2024] [Accepted: 09/11/2024] [Indexed: 09/19/2024]
9
Zhao L, Gong F, Lou K, Wang L, Wang J, Sun H, Wang D, Shi Y, Wang Z. Retrotransposon involves in photoperiodic spermatogenesis in Brandt's voles (Lasiopodomys brandtii) by co-transcription with flagellar genes. Int J Biol Macromol 2024;281:136224. [PMID: 39362423 DOI: 10.1016/j.ijbiomac.2024.136224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 09/10/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024]
10
Decena-Segarra LP, Rovito SM. Transposable Element Diversity and Activity Patterns in Neotropical Salamanders. Mol Biol Evol 2024;41:msae225. [PMID: 39470441 PMCID: PMC11562844 DOI: 10.1093/molbev/msae225] [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: 05/31/2024] [Revised: 09/10/2024] [Accepted: 10/23/2024] [Indexed: 10/30/2024]  Open
11
Sun X, Chen X, Wu B, Zhou L, Chen Y, Zheng S, Wang S, Liu Z. Clam Genome and Transcriptomes Provide Insights into Molecular Basis of Morphological Novelties and Adaptations in Mollusks. BIOLOGY 2024;13:870. [PMID: 39596825 PMCID: PMC11592408 DOI: 10.3390/biology13110870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 10/17/2024] [Accepted: 10/23/2024] [Indexed: 11/29/2024]
12
de Oliveira FS, Azambuja M, Schemberger MO, Nascimento VD, Oliveira JIN, Wolf IR, Nogaroto V, Martins C, Vicari MR. Characterization of hAT DNA transposon superfamily in the genome of Neotropical fish Apareiodon sp. Mol Genet Genomics 2024;299:96. [PMID: 39382723 DOI: 10.1007/s00438-024-02190-x] [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: 12/06/2023] [Accepted: 09/28/2024] [Indexed: 10/10/2024]
13
Duval KL, Artis AR, Goll MG. The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis. Genetics 2024;228:iyae138. [PMID: 39166515 PMCID: PMC11457944 DOI: 10.1093/genetics/iyae138] [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: 07/01/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]  Open
14
Schartl M, Woltering JM, Irisarri I, Du K, Kneitz S, Pippel M, Brown T, Franchini P, Li J, Li M, Adolfi M, Winkler S, de Freitas Sousa J, Chen Z, Jacinto S, Kvon EZ, Correa de Oliveira LR, Monteiro E, Baia Amaral D, Burmester T, Chalopin D, Suh A, Myers E, Simakov O, Schneider I, Meyer A. The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 2024;634:96-103. [PMID: 39143221 PMCID: PMC11514621 DOI: 10.1038/s41586-024-07830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
15
Crepaldi C, Cabral-de-Mello DC, Parise-Maltempi PP. Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. Genome 2024;67:339-350. [PMID: 38739948 DOI: 10.1139/gen-2023-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
16
Zhou C, Zheng X, Wang L, Yue B, DU C, Liu X. The first chromosome-level genome assembly and transcriptome sequencing provide insights into cantharidin production of the blister beetles. Integr Zool 2024;19:929-940. [PMID: 37881135 DOI: 10.1111/1749-4877.12783] [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] [Indexed: 10/27/2023]
17
Gable SM, Bushroe NA, Mendez JM, Wilson A, Pinto BJ, Gamble T, Tollis M. Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles. Genome Biol Evol 2024;16:evae157. [PMID: 39031594 PMCID: PMC11303007 DOI: 10.1093/gbe/evae157] [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: 02/14/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/22/2024]  Open
18
Skalon EK, Panyushev NV, Podgornaya OI, Smolyaninova AR, Solovyeva AI. Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle. Noncoding RNA 2024;10:39. [PMID: 39051373 PMCID: PMC11270206 DOI: 10.3390/ncrna10040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]  Open
19
Dittrich C, Hoelzl F, Smith S, Fouilloux CA, Parker DJ, O’Connell LA, Knowles LS, Hughes M, Fewings A, Morgan R, Rojas B, Comeault AA. Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution. Genome Biol Evol 2024;16:evae109. [PMID: 38753031 PMCID: PMC11152451 DOI: 10.1093/gbe/evae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2024] [Indexed: 06/07/2024]  Open
20
Shao F, Zeng M, Xu X, Zhang H, Peng Z. FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. Database (Oxford) 2024;2024:baae044. [PMID: 38829853 PMCID: PMC11146639 DOI: 10.1093/database/baae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/04/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
21
Münch L, Helmprobst F, Volff JN, Chalopin D, Schartl M, Kneitz S. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus. Genes (Basel) 2024;15:620. [PMID: 38790249 PMCID: PMC11121471 DOI: 10.3390/genes15050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]  Open
22
Wang B, Saleh AA, Yang N, Asare E, Chen H, Wang Q, Chen C, Song C, Gao B. High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes. Animals (Basel) 2024;14:1425. [PMID: 38791643 PMCID: PMC11117352 DOI: 10.3390/ani14101425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]  Open
23
Duval KL, Artis AR, Goll MG. The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.582530. [PMID: 38496550 PMCID: PMC10942377 DOI: 10.1101/2024.03.05.582530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
24
Lin L, Sun T, Guo J, Lin L, Chen M, Wang Z, Bao J, Norvienyeku J, Zhang D, Han Y, Lu G, Rensing C, Zheng H, Zhong Z, Wang Z. Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae. mBio 2024;15:e0008624. [PMID: 38534157 PMCID: PMC11077969 DOI: 10.1128/mbio.00086-24] [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: 01/13/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024]  Open
25
Hassan NT, Galbraith JD, Adelson DL. Multiple horizontal transfer events of a DNA transposon into turtles, fishes, and a frog. Mob DNA 2024;15:7. [PMID: 38605364 PMCID: PMC11008031 DOI: 10.1186/s13100-024-00318-9] [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: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024]  Open
26
Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587621. [PMID: 38617250 PMCID: PMC11014572 DOI: 10.1101/2024.04.01.587621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
27
Villarreal F, Burguener GF, Sosa EJ, Stocchi N, Somoza GM, Turjanski AG, Blanco A, Viñas J, Mechaly AS. Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure. BMC Genomics 2024;25:297. [PMID: 38509481 PMCID: PMC10956332 DOI: 10.1186/s12864-024-10081-z] [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: 07/31/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024]  Open
28
Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024;15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-x] [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: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024]  Open
29
Liang Y, Xian L, Pan J, Zhu K, Guo H, Liu B, Zhang N, Ou-Yang Y, Zhang Q, Zhang D. De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource. Genes (Basel) 2024;15:249. [PMID: 38397238 PMCID: PMC10888354 DOI: 10.3390/genes15020249] [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: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]  Open
30
Gable SM, Bushroe N, Mendez J, Wilson A, Pinto B, Gamble T, Tollis M. Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579686. [PMID: 38405926 PMCID: PMC10888918 DOI: 10.1101/2024.02.09.579686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
31
Souza-Borges CH, Utsunomia R, Varani AM, Uliano-Silva M, Lira LVG, Butzge AJ, Gomez Agudelo JF, Manso S, Freitas MV, Ariede RB, Mastrochirico-Filho VA, Penaloza C, Barria A, Porto-Foresti F, Foresti F, Hattori R, Guiguen Y, Houston RD, Hashimoto DT. De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus. Gigascience 2024;13:giae085. [PMID: 39589439 PMCID: PMC11590113 DOI: 10.1093/gigascience/giae085] [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: 01/15/2024] [Revised: 07/31/2024] [Accepted: 10/14/2024] [Indexed: 11/27/2024]  Open
32
Zhao Y, Su C, He B, Nie R, Wang Y, Ma J, Song J, Yang Q, Hao J. Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome. Nat Commun 2023;14:8190. [PMID: 38081828 PMCID: PMC10713551 DOI: 10.1038/s41467-023-44023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]  Open
33
Chailertrit V, Panthum T, Kongkaew L, Chalermwong P, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Peyachoknagul S, Han K, Srikulnath K. Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus). Genomics Inform 2023;21:e47. [PMID: 38224714 PMCID: PMC10788355 DOI: 10.5808/gi.23075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/17/2024]  Open
34
Xu Y, Tang Y, Feng W, Yang Y, Cui Z. Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023;25:1136-1146. [PMID: 37923816 DOI: 10.1007/s10126-023-10265-w] [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: 08/20/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
35
Dallaire X, Bouchard R, Hénault P, Ulmo-Diaz G, Normandeau E, Mérot C, Bernatchez L, Moore JS. Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication. Genome Biol Evol 2023;15:evad229. [PMID: 38085037 PMCID: PMC10752349 DOI: 10.1093/gbe/evad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2023] [Indexed: 12/28/2023]  Open
36
Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int J Mol Sci 2023;24:16935. [PMID: 38069258 PMCID: PMC10706760 DOI: 10.3390/ijms242316935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]  Open
37
Bush ZD, Naftaly AFS, Dinwiddie D, Albers C, Hillers KJ, Libuda DE. Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages of C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523974. [PMID: 37961628 PMCID: PMC10634987 DOI: 10.1101/2023.01.13.523974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
38
Dionisio JF, Pezenti LF, de Souza RF, Sosa-Gómez DR, da Rosa R. Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution. Mol Genet Genomics 2023;298:1377-1388. [PMID: 37646857 DOI: 10.1007/s00438-023-02063-9] [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: 01/30/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
39
Reinar WB, Tørresen OK, Nederbragt AJ, Matschiner M, Jentoft S, Jakobsen KS. Teleost genomic repeat landscapes in light of diversification rates and ecology. Mob DNA 2023;14:14. [PMID: 37789366 PMCID: PMC10546739 DOI: 10.1186/s13100-023-00302-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]  Open
40
Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023;6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023]  Open
41
DiRusso JA, Clark AT. Transposable elements in early human embryo development and embryo models. Curr Opin Genet Dev 2023;81:102086. [PMID: 37441874 PMCID: PMC10917458 DOI: 10.1016/j.gde.2023.102086] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
42
Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Krylov V, Kubíčková S, Fokam EB, Badjedjea G, Evans BJ, Knytl M. Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae). EUR J WILDLIFE RES 2023;69:81. [PMID: 37483536 PMCID: PMC10361878 DOI: 10.1007/s10344-023-01709-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/13/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
43
Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023;24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023]  Open
44
Gable SM, Mendez JM, Bushroe NA, Wilson A, Byars MI, Tollis M. The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order. Genes (Basel) 2023;14:1387. [PMID: 37510292 PMCID: PMC10379679 DOI: 10.3390/genes14071387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]  Open
45
Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol 2023;21:145. [PMID: 37365567 DOI: 10.1186/s12915-023-01632-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023]  Open
46
Paulat NS, Storer JM, Moreno-Santillán DD, Osmanski AB, Sullivan KAM, Grimshaw JR, Korstian J, Halsey M, Garcia CJ, Crookshanks C, Roberts J, Smit AFA, Hubley R, Rosen J, Teeling EC, Vernes SC, Myers E, Pippel M, Brown T, Hiller M, Rojas D, Dávalos LM, Lindblad-Toh K, Karlsson EK, Ray DA. Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia. Mol Biol Evol 2023;40:msad092. [PMID: 37071810 PMCID: PMC10162687 DOI: 10.1093/molbev/msad092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 04/20/2023]  Open
47
Zhou J, Hu J, Wang Y, Gao S. Induction and application of human naive pluripotency. Cell Rep 2023;42:112379. [PMID: 37043354 DOI: 10.1016/j.celrep.2023.112379] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/18/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023]  Open
48
Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023;33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
49
Carotti E, Tittarelli E, Canapa A, Biscotti MA, Carducci F, Barucca M. LTR Retroelements and Bird Adaptation to Arid Environments. Int J Mol Sci 2023;24:ijms24076332. [PMID: 37047324 PMCID: PMC10094322 DOI: 10.3390/ijms24076332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]  Open
50
Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023;32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
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