Divergence of 3′ ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae

Abstract

SummaryShort 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.

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

“…The similarities include both, repeat family and abundance. In line with evidence from other conifers (Prunier et al, 2016), these results also suggest the limited TE elimination, usually carried out by recombination, reshuffling, fragmentation, or removal as aftermath to genomic rearrangements (Ma et al, 2004;Ren et al, 2018;Kögler et al, 2020;Maiwald et al, 2021;Schmidt et al, 2021). Along the same lines, we did not observe any transpositional bursts of amplification during the speciation of the larches.…”

Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only few fast-evolving satellite DNAs

“…The similarities include both, repeat family and abundance. In line with evidence from other conifers (Prunier et al, 2016), these results also suggest the limited TE elimination, usually carried out by recombination, reshuffling, or removal as aftermath to genomic rearrangements (Ma et al, 2004;Ren et al, 2018;Kögler et al, 2020;Maiwald et al, 2020). Along the same lines, we did not observe any transpositional bursts of amplification during the speciation of the larches.…”

Application of retrotransposon-based Inter-SINE Amplified Polymorphism (ISAP) markers for the differentiation of common poplar genotypes

“…The genome sequence of Populus tremula (plantgenie.org, v1.1) was analyzed for the presence of SINE sequences using the software SINE-Finder (Wenke et al 2011). The respective results have been published separately by Koegler et al (2020). A manually optimized alignment of full-length SINE sequences formed the basis for the assignment of individual SINEs to families based on their pairwise identity to a family consensus.…”

“…A total of eight SINE (sub-) families with over 4,400 full-length copies were identified in the Populus tremula genome (Koegler et al 2020). The length of the representative consensus sequences ranges from 163 bp to 241 bp (Table 3).…”

“…Here, we establish the ISAP marker system in poplars to offer a robust, efficient, and easy method for the identification and differentiation of different poplar accessions. The recent identification and characterization of several SINE families in poplar and related genomes allowed us to establish ISAP markers in poplar (Koegler et al 2020). Due to the genome-wide distribution of poplar SINEs, their high copy number and their family specific structure, the derived markers generate informative fingerprint-like banding patterns, valuable for genotype differentiation in poplar.…”