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Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome.
Mol Genet Genomics. 2010 Mar; 283(3):255-71.MG

Abstract

Retrotransposons constitute a major proportion of the Triticeae genomes. Genome-scale studies have revealed their role in evolution affecting both genome structure and function and their potential for the development of novel markers. In this study, family members of an LTR copia retrotransposon which mediated the duplication of the gene encoding the high molecular weight glutenin subunit Bx7 in cultivar Glenlea were characterized. This novel element was named Sasanda_EU157184-1 (TREP3516). High density filters of the Glenlea hexaploid wheat BAC library were screened with a Sasanda long terminal repeat (LTR)-specific probe and approximately 1,075 positive clones representing an estimated copy number of 347 elements per haploid genome were identified. The 242 BAC clones with the strongest hybridization signal were selected. To maximize isolation of complete elements, this subset of clones was screened with a reverse transcriptase (RT) domain probe and DNA was isolated from the 133 clones that produced a strong hybridization signal. Left (5') and right (3') LTRs as well as the RT domains were PCR amplified and sequencing was carried out on the final subset of 121 clones. Evolutionary relationships were inferred from a data set consisting of 100 RT, 102 5' LTR and 100 3' LTR sequences representing 233, 451 and 495 informative sites for comparison, respectively. Neighbour-joining tree indicated that the element is at least 1.8 million years old and has evolved into a minimum of five sub-families. The insertion times of the 89 complete elements were estimated based on the divergence between their LTRs. Corroborating the inference from the RT domain, analysis of the LTR domains also indicated bursts of amplification from 2.6 million years ago (MYA) to now, except for one member dated to 4.6 +/- 0.7 MYA, which corresponds to the interval of divergence of Triticum and Aegilops (3 MYA) and divergence of Triticum and Rye (7 MYA). In 44 elements, the 5' and 3' LTRs were identical indicating recent transposition activity. The element can be used to develop retrotransposon-based markers such as sequence-specific amplified polymorphism, retrotransposon microsatellite amplified polymorphism and inter-retrotransposon amplified polymorphism, all of which are well suited for genotyping studies.

Authors+Show Affiliations

Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada.No affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

20127492

Citation

Ragupathy, Raja, et al. "Molecular Characterization of the Sasanda LTR Copia Retrotransposon Family Uncovers Their Recent Amplification in Triticum Aestivum (L.) Genome." Molecular Genetics and Genomics : MGG, vol. 283, no. 3, 2010, pp. 255-71.
Ragupathy R, Banks T, Cloutier S. Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome. Mol Genet Genomics. 2010;283(3):255-71.
Ragupathy, R., Banks, T., & Cloutier, S. (2010). Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome. Molecular Genetics and Genomics : MGG, 283(3), 255-71. https://doi.org/10.1007/s00438-009-0509-8
Ragupathy R, Banks T, Cloutier S. Molecular Characterization of the Sasanda LTR Copia Retrotransposon Family Uncovers Their Recent Amplification in Triticum Aestivum (L.) Genome. Mol Genet Genomics. 2010;283(3):255-71. PubMed PMID: 20127492.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome. AU - Ragupathy,Raja, AU - Banks,Travis, AU - Cloutier,Sylvie, Y1 - 2010/02/03/ PY - 2009/09/08/received PY - 2009/12/24/accepted PY - 2010/2/4/entrez PY - 2010/2/4/pubmed PY - 2010/5/1/medline SP - 255 EP - 71 JF - Molecular genetics and genomics : MGG JO - Mol. Genet. Genomics VL - 283 IS - 3 N2 - Retrotransposons constitute a major proportion of the Triticeae genomes. Genome-scale studies have revealed their role in evolution affecting both genome structure and function and their potential for the development of novel markers. In this study, family members of an LTR copia retrotransposon which mediated the duplication of the gene encoding the high molecular weight glutenin subunit Bx7 in cultivar Glenlea were characterized. This novel element was named Sasanda_EU157184-1 (TREP3516). High density filters of the Glenlea hexaploid wheat BAC library were screened with a Sasanda long terminal repeat (LTR)-specific probe and approximately 1,075 positive clones representing an estimated copy number of 347 elements per haploid genome were identified. The 242 BAC clones with the strongest hybridization signal were selected. To maximize isolation of complete elements, this subset of clones was screened with a reverse transcriptase (RT) domain probe and DNA was isolated from the 133 clones that produced a strong hybridization signal. Left (5') and right (3') LTRs as well as the RT domains were PCR amplified and sequencing was carried out on the final subset of 121 clones. Evolutionary relationships were inferred from a data set consisting of 100 RT, 102 5' LTR and 100 3' LTR sequences representing 233, 451 and 495 informative sites for comparison, respectively. Neighbour-joining tree indicated that the element is at least 1.8 million years old and has evolved into a minimum of five sub-families. The insertion times of the 89 complete elements were estimated based on the divergence between their LTRs. Corroborating the inference from the RT domain, analysis of the LTR domains also indicated bursts of amplification from 2.6 million years ago (MYA) to now, except for one member dated to 4.6 +/- 0.7 MYA, which corresponds to the interval of divergence of Triticum and Aegilops (3 MYA) and divergence of Triticum and Rye (7 MYA). In 44 elements, the 5' and 3' LTRs were identical indicating recent transposition activity. The element can be used to develop retrotransposon-based markers such as sequence-specific amplified polymorphism, retrotransposon microsatellite amplified polymorphism and inter-retrotransposon amplified polymorphism, all of which are well suited for genotyping studies. SN - 1617-4623 UR - https://www.unboundmedicine.com/medline/citation/20127492/Molecular_characterization_of_the_Sasanda_LTR_copia_retrotransposon_family_uncovers_their_recent_amplification_in_Triticum_aestivum__L___genome_ L2 - https://dx.doi.org/10.1007/s00438-009-0509-8 DB - PRIME DP - Unbound Medicine ER -