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Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization.
Mol Genet Genomics. 2010 Jul; 284(1):11-23.MG

Abstract

Mobile elements constitute a considerable part of the eukaryotic genome. This work is focused on the distribution and evolution of DNA-transposons in the genomes of diploid and allopolyploid Triticeae species and their role in the formation of functionally important chromosomal subtelomeric regions. The Caspar family is among the most abundant of CACTA DNA-transposons in Triticeae. To study the evolution of Caspar-like elements in Triticeae genomes, we analyzed their sequences and distribution in chromosomes by in situ hybridization. In total, 46 Caspar-like elements from the wheat and barley Caspar, Clifford, and Donald families were analyzed after being extracted from databases using the transposase consensus sequence. Sequence alignment and subsequent phylogenetic analyses revealed that the transposase DNA sequences formed three major distinct groups: (1) Clifford, (2) Caspar_Triticinae, and (3) Caspar_Hordeinae. Additionally, in situ hybridization demonstrated that Caspar_Triticinae transposons are predominantly compartmentalized in the subtelomeric chromosomal regions of wheat and its progenitors. Analysis of data suggested that compartmentalization in the subtelomeric chromosomal region was a characteristic feature of all the main groups of Caspar-like elements. Furthermore, a dot plot analysis of the terminal repeats demonstrated that the divergence of these repeats strictly correlated with the divergence of Caspar coding sequences. A clear distinction in the Caspar DNA sequences among the species Triticum/Aegilops (Caspar_Triticinae), Hordeum (Caspar_Hordeinae), and different distributions in individual hexaploid wheat genomes (A/B and D) suggest an independent proliferation of these elements in wheat (or its progenitors) and barley genomes. Thus, Caspar-like transposons can significantly contribute to the formation and differentiation of subtelomeric regions in Triticeae species.

Authors+Show Affiliations

Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia. sergeeva@bionet.nsc.ruNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

20512353

Citation

Sergeeva, Ekaterina M., et al. "Evolutionary Analysis of the CACTA DNA-transposon Caspar Across Wheat Species Using Sequence Comparison and in Situ Hybridization." Molecular Genetics and Genomics : MGG, vol. 284, no. 1, 2010, pp. 11-23.
Sergeeva EM, Salina EA, Adonina IG, et al. Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization. Mol Genet Genomics. 2010;284(1):11-23.
Sergeeva, E. M., Salina, E. A., Adonina, I. G., & Chalhoub, B. (2010). Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization. Molecular Genetics and Genomics : MGG, 284(1), 11-23. https://doi.org/10.1007/s00438-010-0544-5
Sergeeva EM, et al. Evolutionary Analysis of the CACTA DNA-transposon Caspar Across Wheat Species Using Sequence Comparison and in Situ Hybridization. Mol Genet Genomics. 2010;284(1):11-23. PubMed PMID: 20512353.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization. AU - Sergeeva,Ekaterina M, AU - Salina,Elena A, AU - Adonina,Irina G, AU - Chalhoub,Boulos, Y1 - 2010/05/29/ PY - 2009/10/28/received PY - 2010/05/04/accepted PY - 2010/6/1/entrez PY - 2010/6/1/pubmed PY - 2010/6/30/medline SP - 11 EP - 23 JF - Molecular genetics and genomics : MGG JO - Mol Genet Genomics VL - 284 IS - 1 N2 - Mobile elements constitute a considerable part of the eukaryotic genome. This work is focused on the distribution and evolution of DNA-transposons in the genomes of diploid and allopolyploid Triticeae species and their role in the formation of functionally important chromosomal subtelomeric regions. The Caspar family is among the most abundant of CACTA DNA-transposons in Triticeae. To study the evolution of Caspar-like elements in Triticeae genomes, we analyzed their sequences and distribution in chromosomes by in situ hybridization. In total, 46 Caspar-like elements from the wheat and barley Caspar, Clifford, and Donald families were analyzed after being extracted from databases using the transposase consensus sequence. Sequence alignment and subsequent phylogenetic analyses revealed that the transposase DNA sequences formed three major distinct groups: (1) Clifford, (2) Caspar_Triticinae, and (3) Caspar_Hordeinae. Additionally, in situ hybridization demonstrated that Caspar_Triticinae transposons are predominantly compartmentalized in the subtelomeric chromosomal regions of wheat and its progenitors. Analysis of data suggested that compartmentalization in the subtelomeric chromosomal region was a characteristic feature of all the main groups of Caspar-like elements. Furthermore, a dot plot analysis of the terminal repeats demonstrated that the divergence of these repeats strictly correlated with the divergence of Caspar coding sequences. A clear distinction in the Caspar DNA sequences among the species Triticum/Aegilops (Caspar_Triticinae), Hordeum (Caspar_Hordeinae), and different distributions in individual hexaploid wheat genomes (A/B and D) suggest an independent proliferation of these elements in wheat (or its progenitors) and barley genomes. Thus, Caspar-like transposons can significantly contribute to the formation and differentiation of subtelomeric regions in Triticeae species. SN - 1617-4623 UR - https://www.unboundmedicine.com/medline/citation/20512353/Evolutionary_analysis_of_the_CACTA_DNA_transposon_Caspar_across_wheat_species_using_sequence_comparison_and_in_situ_hybridization_ L2 - https://doi.org/10.1007/s00438-010-0544-5 DB - PRIME DP - Unbound Medicine ER -