The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution
2015 (English)In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 568, no 1, 89-99 p.Article in journal (Refereed) Published
Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10 s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. (C) 2015 Elsevier B.V. All rights reserved.
Place, publisher, year, edition, pages
2015. Vol. 568, no 1, 89-99 p.
LTR retrotransposon, Ty1-copia, PARTC, Gymnosperms, Conifers, Picea, Pinus, Abies, Taxus, Juniperus, Ginkgo
Evolutionary Biology Genetics
IdentifiersURN: urn:nbn:se:uu:diva-259632DOI: 10.1016/j.gene.2015.05.028ISI: 000357439000015PubMedID: 25982862OAI: oai:DiVA.org:uu-259632DiVA: diva2:847765
FunderKnut and Alice Wallenberg Foundation
Funding: Scuola Superiore Sant'Anna, Pisa, Italy A6013AZ2015-08-212015-08-102015-08-21Bibliographically approved