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For: Kalendar R, Raskina O, Belyayev A, Schulman AH. Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants. Int J Mol Sci 2020;21:ijms21082931. [PMID: 32331257 PMCID: PMC7215508 DOI: 10.3390/ijms21082931] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023]  Open
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
Kalendar R, Shevtsov A, Otarbay Z, Ismailova A. In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays. FRONTIERS IN BIOINFORMATICS 2024;4:1464197. [PMID: 39435190 PMCID: PMC11491563 DOI: 10.3389/fbinf.2024.1464197] [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: 07/13/2024] [Accepted: 09/17/2024] [Indexed: 10/23/2024]  Open
3
Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024;41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024]  Open
4
Kojima KK. Helenus and Ajax, Two Groups of Non-Autonomous LTR Retrotransposons, Represent a New Type of Small RNA Gene-Derived Mobile Elements. BIOLOGY 2024;13:119. [PMID: 38392337 PMCID: PMC10886601 DOI: 10.3390/biology13020119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
5
Maiwald S, Mann L, Garcia S, Heitkam T. Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes. Mol Biol Evol 2024;41:msae010. [PMID: 38262464 PMCID: PMC10853983 DOI: 10.1093/molbev/msae010] [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: 07/21/2023] [Revised: 10/26/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024]  Open
6
Yang X, Huang K, Yang D, Zhao W, Zhou X. Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review. GLOBAL CHALLENGES (HOBOKEN, NJ) 2024;8:2300163. [PMID: 38223896 PMCID: PMC10784210 DOI: 10.1002/gch2.202300163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/20/2023] [Indexed: 01/16/2024]
7
Kalendar R, Karlov GI. Editorial: Mobile elements and plant genome evolution, comparative analyses and computational tools, volume II. FRONTIERS IN PLANT SCIENCE 2023;14:1308536. [PMID: 38023887 PMCID: PMC10676221 DOI: 10.3389/fpls.2023.1308536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023]
8
Arvas YE, Marakli S, Kaya Y, Kalendar R. The power of retrotransposons in high-throughput genotyping and sequencing. FRONTIERS IN PLANT SCIENCE 2023;14:1174339. [PMID: 37180380 PMCID: PMC10167742 DOI: 10.3389/fpls.2023.1174339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
9
Divashuk MG, Nikitina EA, Sokolova VM, Yurkina AI, Kocheshkova AA, Razumova OV, Karlov GI, Kroupin PY. qPCR as a Selective Tool for Cytogenetics. PLANTS (BASEL, SWITZERLAND) 2022;12:80. [PMID: 36616209 PMCID: PMC9824742 DOI: 10.3390/plants12010080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
10
Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou L, Ahmad Z, Vinod KK, Yang P, Zhou M. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. FRONTIERS IN PLANT SCIENCE 2022;13:1064847. [PMID: 36570931 PMCID: PMC9780303 DOI: 10.3389/fpls.2022.1064847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
11
Transposable Elements in the Revealing of Polymorphism-Based Differences in the Seeds of Flax Varieties Grown in Remediated Chernobyl Area. PLANTS 2022;11:plants11192567. [PMID: 36235434 PMCID: PMC9571286 DOI: 10.3390/plants11192567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
12
Yucel G, Betekhtin A, Cabi E, Tuna M, Hasterok R, Kolano B. The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae). Int J Mol Sci 2022;23:ijms231911033. [PMID: 36232345 PMCID: PMC9570107 DOI: 10.3390/ijms231911033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 02/02/2023]  Open
13
Li F, Lee M, Esnault C, Wendover K, Guo Y, Atkins P, Zaratiegui M, Levin HL. Identification of an integrase-independent pathway of retrotransposition. SCIENCE ADVANCES 2022;8:eabm9390. [PMID: 35767609 DOI: 10.1126/sciadv.abm9390] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
14
Lerat E. Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements. Front Genet 2022;13:891194. [PMID: 35646069 PMCID: PMC9140218 DOI: 10.3389/fgene.2022.891194] [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: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022]  Open
15
Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato. Int J Mol Sci 2022;23:ijms23073643. [PMID: 35409003 PMCID: PMC8998684 DOI: 10.3390/ijms23073643] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023]  Open
16
Kalendar R. A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021;2392:223-243. [PMID: 34773626 DOI: 10.1007/978-1-0716-1799-1_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
17
The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021;22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023]  Open
18
Kalendar R, Sabot F, Rodriguez F, Karlov GI, Natali L, Alix K. Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools. FRONTIERS IN PLANT SCIENCE 2021;12:735134. [PMID: 34630484 PMCID: PMC8500305 DOI: 10.3389/fpls.2021.735134] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/30/2021] [Indexed: 05/28/2023]
19
Orłowska R, Pachota KA, Dynkowska WM, Niedziela A, Bednarek PT. Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley. Int J Mol Sci 2021;22:ijms22136783. [PMID: 34202586 PMCID: PMC8268840 DOI: 10.3390/ijms22136783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023]  Open
20
Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity. Methods Mol Biol 2021;2222:263-286. [PMID: 33301099 DOI: 10.1007/978-1-0716-0997-2_15] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
21
Erper I, Ozer G, Kalendar R, Avci S, Yildirim E, Alkan M, Turkkan M. Genetic Diversity and Pathogenicity of Rhizoctonia spp. Isolates Associated with Red Cabbage in Samsun (Turkey). J Fungi (Basel) 2021;7:jof7030234. [PMID: 33801129 PMCID: PMC8004240 DOI: 10.3390/jof7030234] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/31/2023]  Open
22
Khapilina O, Raiser O, Danilova A, Shevtsov V, Turzhanova A, Kalendar R. DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai. PeerJ 2021;9:e10674. [PMID: 33510974 PMCID: PMC7798630 DOI: 10.7717/peerj.10674] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022]  Open
23
Maiwald S, Weber B, Seibt KM, Schmidt T, Heitkam T. The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability. ANNALS OF BOTANY 2021;127:91-109. [PMID: 33009553 PMCID: PMC7750724 DOI: 10.1093/aob/mcaa176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 05/26/2023]
24
Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes (Basel) 2020;11:genes11101216. [PMID: 33081418 PMCID: PMC7602945 DOI: 10.3390/genes11101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]  Open
25
Turzhanova A, Khapilina ON, Tumenbayeva A, Shevtsov V, Raiser O, Kalendar R. Genetic diversity of Alternaria species associated with black point in wheat grains. PeerJ 2020;8:e9097. [PMID: 32411537 PMCID: PMC7207207 DOI: 10.7717/peerj.9097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022]  Open
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