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Divergence of 3′ ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae
Author(s) -
Kögler Anja,
Seibt Kathrin M.,
Heitkam Tony,
Morgenstern Kristin,
Reiche Birgit,
Brückner Marie,
Wolf Heino,
Krabel Doris,
Schmidt Thomas
Publication year - 2020
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.14721
Subject(s) - salicaceae , populus trichocarpa , biology , evolutionary biology , phylogenetic tree , sine , deciduous , botany , phylogenetics , genome , woody plant , genetics , gene , geometry , mathematics
Summary Short interspersed nuclear elements (SINEs) are small, non‐autonomous and heterogeneous retrotransposons that are widespread in plants. To explore the amplification dynamics and evolutionary history of SINE populations in representative deciduous tree species, we analyzed the genomes of the six following Salicaceae species: Populus deltoides , Populus euphratica , Populus tremula , Populus tremuloides , Populus trichocarpa , and Salix purpurea . We identified 11 Salicaceae SINE families (SaliS‐I to SaliS‐XI), comprising 27 077 full‐length copies. Most of these families harbor segmental similarities, providing evidence for SINE emergence by reshuffling or heterodimerization. We observed two SINE groups, differing in phylogenetic distribution pattern, similarity and 3′ end structure. These groups probably emerged during the ‘salicoid duplication’ (~65 million years ago) in the Salix – Populus progenitor and during the separation of the genus Salix (45–65 million years ago), respectively. In contrast to conserved 5′ start motifs across species and SINE families, the 3′ ends are highly variable in sequence and length. This extraordinary 3′‐end variability results from mutations in the poly(A) tail, which were fixed by subsequent amplificational bursts. We show that the dissemination of newly evolved 3′ ends is accomplished by a displacement of older motifs, leading to various 3′‐end subpopulations within the SaliS families.