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For: Sproul JS, Hotaling S, Heckenhauer J, Powell A, Marshall D, Larracuente AM, Kelley JL, Pauls SU, Frandsen PB. Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges. Genome Res 2023;33:1708-1717. [PMID: 37739812 PMCID: PMC10691545 DOI: 10.1101/gr.277387.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 09/20/2023] [Indexed: 09/24/2023]
Number Cited by Other Article(s)
1
Kalendar R, Kairov U. Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats. Bioinform Biol Insights 2024;18:11779322241306391. [PMID: 39703748 PMCID: PMC11656428 DOI: 10.1177/11779322241306391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 11/25/2024] [Indexed: 12/21/2024]  Open
2
Parisot N, Ribeiro Lopes M, Peignier S, Baa-Puyoulet P, Charles H, Calevro F, Callaerts P. Annotation of transcription factors, chromatin-associated factors, and basal transcription machinery in the pea aphid, Acyrthosiphon pisum, and development of the ATFdb database, a resource for studies of transcriptional regulation. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024;177:104217. [PMID: 39579797 DOI: 10.1016/j.ibmb.2024.104217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 10/15/2024] [Accepted: 11/19/2024] [Indexed: 11/25/2024]
3
Wattad H, Molcho J, Manor R, Weil S, Aflalo ED, Chalifa-Caspi V, Sagi A. Roadmap and Considerations for Genome Editing in a Non-Model Organism: Genetic Variations and Off-Target Profiling. Int J Mol Sci 2024;25:12530. [PMID: 39684244 DOI: 10.3390/ijms252312530] [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: 09/29/2024] [Revised: 11/14/2024] [Accepted: 11/18/2024] [Indexed: 12/18/2024]  Open
4
Yuan H, Liu XJ, Liu XZ, Zhao LN, Mao SL, Huang Y. The evolutionary dynamics of genome sizes and repetitive elements in Ensifera (Insecta: Orthoptera). BMC Genomics 2024;25:1041. [PMID: 39501135 PMCID: PMC11539627 DOI: 10.1186/s12864-024-10949-0] [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: 06/07/2024] [Accepted: 10/24/2024] [Indexed: 11/08/2024]  Open
5
Martelossi J, Iannello M, Ghiselli F, Luchetti A. Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions. Mob DNA 2024;15:22. [PMID: 39415259 PMCID: PMC11481361 DOI: 10.1186/s13100-024-00332-x] [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: 02/14/2024] [Accepted: 10/03/2024] [Indexed: 10/18/2024]  Open
6
Weng YM, Lopez-Cacacho I, Foquet B, Martinez JI, Plotkin D, Sourakov A, Frandsen PB, Kawahara AY. A near chromosome-level genome assembly of a ghost moth (Lepidoptera, Hepialidae). Sci Data 2024;11:1139. [PMID: 39414832 PMCID: PMC11484951 DOI: 10.1038/s41597-024-03783-2] [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: 02/26/2024] [Accepted: 08/14/2024] [Indexed: 10/18/2024]  Open
7
Cicconardi F, Morris BJ, Martelossi J, Ray DA, Montgomery SH. Novel Sex-Specific Genes and Diverse Interspecific Expression in the Antennal Transcriptomes of Ithomiine Butterflies. Genome Biol Evol 2024;16:evae218. [PMID: 39373182 PMCID: PMC11500719 DOI: 10.1093/gbe/evae218] [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: 06/11/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/08/2024]  Open
8
Ye X, Yang Y, Zhao X, Fang Q, Ye G. The state of parasitoid wasp genomics. Trends Parasitol 2024;40:914-929. [PMID: 39227194 DOI: 10.1016/j.pt.2024.08.003] [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: 06/26/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
9
Betancourt AJ, Wei KHC, Huang Y, Lee YCG. Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective. Annu Rev Genomics Hum Genet 2024;25:1-25. [PMID: 38603565 DOI: 10.1146/annurev-genom-120822-105708] [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: 04/13/2024]
10
Majid M, Khan H, Liu X, Shaheer M, Huang Y. Evolutionary Dynamics of Satellite DNA Repeats across the Tettigoniidae Family: Insights from Genomic Analysis. Biomolecules 2024;14:915. [PMID: 39199303 PMCID: PMC11352069 DOI: 10.3390/biom14080915] [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: 05/17/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/01/2024]  Open
11
Schweizer RM, Meidt CG, Benavides LR, Wilson JS, Griswold TL, Sim SB, Geib SM, Branstetter MG. Reference genome for the Mojave poppy bee (Perdita meconis), a specialist pollinator of conservation concern. J Hered 2024;115:470-479. [PMID: 38088446 PMCID: PMC11235129 DOI: 10.1093/jhered/esad076] [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: 09/15/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 07/11/2024]  Open
12
Wang Q, Zhang J, Liu C, Ru C, Qian Q, Yang M, Yan S, Liu W, Wang G. Identification of antennal alternative splicing by combining genome and full-length transcriptome analysis in Bactrocera dorsalis. Front Physiol 2024;15:1384426. [PMID: 38952867 PMCID: PMC11215311 DOI: 10.3389/fphys.2024.1384426] [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: 02/09/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024]  Open
13
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]
14
Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024;2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [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: 06/01/2024]
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