title: The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.
abstract: 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 10s 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.
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy; Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy. Electronic address: a.zuccolo@sssup.it.
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-75236 Uppsala, Sweden.
authors.forename: Douglas G
authors.initials: DG
authors.lastname: Scofield
authors.affiliation: Università degli Studi di Udine, Via delle Scienze 208, 33100 Udine, Italy.
authors.forename: Emanuele
authors.initials: E
authors.lastname: De Paoli
authors.affiliation: Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy; Università degli Studi di Udine, Via delle Scienze 208, 33100 Udine, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
mesh_terms: D017124:Conserved Sequence; D019143:Evolution, Molecular; D005784:Gene Amplification; D017343:Genes, Plant; D010802:Phylogeny; D018626:Retroelements; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences; D064028:Tracheophyta / Q000235:genetics*
chemical_list: D018626:Retroelements
keywords: Abies; Conifers; Ginkgo; Gymnosperms; Juniperus; LTR retrotransposon; PARTC; Picea; Pinus; Taxus; Ty1-copia