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.

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Early above- and belowground biomass fractionation, root diameter composition and allocation of cumulated fine root length per total leaf area of Populus clones have been measured for a pre-assessment of the risk for plantation establishment during spring drought conditions. Four clones of Populus × euramericana, and one P. nigra × P. maximowiczii clone (cv. Max 3), were planted in sandy mix substrate and were exposed to one normal and one deficit watering regime over 65-day greenhouse experiments conducted during early summer. The P. × euramericana hybrids showed plasticity of their root biomass fractions. Although clone Max 3 was among the productive clones, even under deficit watering, it was not able to respond plastically to deficit watering. It showed no increase in the root biomass fraction and no increase in the ratio of cumulated fine root length per total leaf area. Therefore, the clone Max 3 should not be planted under high risk for spring drought. Planting the investigated P. × euramericana clones under water deficit likely involves a lower risk, but clone differences within this group must be considered. It can be concluded that the water deficit response of biomass allocation to roots and of the ratio of fine root length per unit leaf area is suitable traits to improve drought risk assessments that are based on yield response of poplar clones to drought. Percent plant loss data and the yield at the end of the first SRC rotation will be suitable to verify the present greenhouse assessment.

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In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers’ accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs’ organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

Knowledge of the ecology and biology of Rhabdocline pseudotsugae Sydow is still at a very early stage. Recent results indicate the existence of an endophytic stage of the fungus in the form of symptomless infections in various Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) tissue types. This study represents the first description of genetic variation between and within two populations of R. pseudotsugae. Needles featuring fruiting bodies of R. pseudotsugae were collected from sample areas in Saxony and North Rhine-Westphalia (in Germany), with different fungal genotypes distinguished using the start codon targeted polymorphism (SCoT) and branch point signal sequences (BPS) techniques. Five of the 20 primers tested could be selected for further investigation. A total of 349 fragments were amplified at an average of 69.8 fragments per primer. Results showed the two sample areas to exhibit a high degree of both genetic variability and genetic diversity. A clear differentiation between the sample areas was not observed. There was nevertheless a clear connection between the genetic distance and spatial distribution of the fruiting bodies of R. pseudotsugae within the sample areas themselves.

On the basis of retrotransposon-insertion polymorphisms, molecular markers were developed for the identification and differentiation of poplar (<i>Populus</i> spp.) genotypes. For this purpose, short interspersed nuclear elements (SINEs) in the genome sequence of <i>Populus tremula</i> were identified and assigned to different SINE-families. For families with high copy number and high identity values, primers were derived to amplify Inter- SINE Amplified Polymorphisms (ISAPs) with polymerase chain reaction (PCR). The resulting fragments produce genotype-specific fingerprints. This molecular approach utilizes standard laboratory equipment and is therefore easy to use for the verification of plant material. We demonstrate the functionality of three distinct ISAP primer combinations by comparison to ten simple sequence repeat (SSR) markers to differentiate 23 poplar genotypes. Already by using a single ISAP primer combination all genotypes can be clearly discriminated. Furthermore, the cluster analysis based on three primer combinations divides clones according to their genetic background into two subclusters (by a bootstrap value of 98). Our results clearly demonstrate the usability of ISAP markers to differentiate genotypes and trace progenies of poplar trees.

In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 gigabasepairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.