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Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers.
Mol Biol Evol. 2001 Jul; 18(7):1176-88.MB

Abstract

We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.

Authors+Show Affiliations

Botanical Garden of the University of Osnabrück, Osnabrück, Germany.No affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

11420359

Citation

Friesen, N, et al. "Diversity, Origin, and Distribution of Retrotransposons (gypsy and Copia) in Conifers." Molecular Biology and Evolution, vol. 18, no. 7, 2001, pp. 1176-88.
Friesen N, Brandes A, Heslop-Harrison JS. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol. 2001;18(7):1176-88.
Friesen, N., Brandes, A., & Heslop-Harrison, J. S. (2001). Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Molecular Biology and Evolution, 18(7), 1176-88.
Friesen N, Brandes A, Heslop-Harrison JS. Diversity, Origin, and Distribution of Retrotransposons (gypsy and Copia) in Conifers. Mol Biol Evol. 2001;18(7):1176-88. PubMed PMID: 11420359.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. AU - Friesen,N, AU - Brandes,A, AU - Heslop-Harrison,J S, PY - 2001/6/23/pubmed PY - 2001/9/28/medline PY - 2001/6/23/entrez SP - 1176 EP - 88 JF - Molecular biology and evolution JO - Mol Biol Evol VL - 18 IS - 7 N2 - We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants. SN - 0737-4038 UR - https://www.unboundmedicine.com/medline/citation/11420359/Diversity_origin_and_distribution_of_retrotransposons__gypsy_and_copia__in_conifers_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/oxfordjournals.molbev.a003905 DB - PRIME DP - Unbound Medicine ER -