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Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae).
Plant Cell Rep. 2013 Oct; 32(10):1575-88.PC

Abstract

KEY MESSAGE

High heterogeneity was observed among conserved domains of reverse transcriptase (rt) isolated from quinoa. Only one Ty1- copia rt was highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes. The heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.

Authors+Show Affiliations

Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland, bozena.kolano@us.edu.pl.No affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

23754338

Citation

Kolano, Bozena, et al. "Isolation and Characterization of Reverse Transcriptase Fragments of LTR Retrotransposons From the Genome of Chenopodium Quinoa (Amaranthaceae)." Plant Cell Reports, vol. 32, no. 10, 2013, pp. 1575-88.
Kolano B, Bednara E, Weiss-Schneeweiss H. Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae). Plant Cell Rep. 2013;32(10):1575-88.
Kolano, B., Bednara, E., & Weiss-Schneeweiss, H. (2013). Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae). Plant Cell Reports, 32(10), 1575-88. https://doi.org/10.1007/s00299-013-1468-4
Kolano B, Bednara E, Weiss-Schneeweiss H. Isolation and Characterization of Reverse Transcriptase Fragments of LTR Retrotransposons From the Genome of Chenopodium Quinoa (Amaranthaceae). Plant Cell Rep. 2013;32(10):1575-88. PubMed PMID: 23754338.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae). AU - Kolano,Bozena, AU - Bednara,Edyta, AU - Weiss-Schneeweiss,Hanna, Y1 - 2013/06/11/ PY - 2013/01/30/received PY - 2013/05/28/accepted PY - 2013/04/30/revised PY - 2013/6/12/entrez PY - 2013/6/12/pubmed PY - 2014/2/11/medline SP - 1575 EP - 88 JF - Plant cell reports JO - Plant Cell Rep. VL - 32 IS - 10 N2 - KEY MESSAGE: High heterogeneity was observed among conserved domains of reverse transcriptase (rt) isolated from quinoa. Only one Ty1- copia rt was highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes. The heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics. SN - 1432-203X UR - https://www.unboundmedicine.com/medline/citation/23754338/Isolation_and_characterization_of_reverse_transcriptase_fragments_of_LTR_retrotransposons_from_the_genome_of_Chenopodium_quinoa__Amaranthaceae__ L2 - http://dx.doi.org/10.1007/s00299-013-1468-4 DB - PRIME DP - Unbound Medicine ER -