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The genus Leymus (lymegrass) comprises about 30 polyploid, perennial, temperate grass species in the tribe Triticeae (family Poaceae). Previous studies indicated a large diversity in the Leymus genome, and therefore, the aim of this study was to isolate new repetitive DNA sequences that can be used for differentiating Leymus species and elucidating their genomic relationships. A [C.sub.0]t-1 DNA plasmid library was generated from genomic DNA of American tetraploid species Leymus triticoides. A family of highly repetitive satellite DNA sequences, designated Lt1, was obtained from this library. The Lt1 family consisted of 380 by SacI repeating units arranging in tandem arrays. A 120 by MspI subfamily was discovered within this family, indicating that cytosine methylation may have played an important role in the evolution of satellite sequences. The Lt1 satellite was localized in the subtelomeric heterochromatic blocks of L. triticoides chromosomes, which are present on all chromosomes and often on both arms. The Lt1 sequences are abundant in L. triticoides but absent in its closely related species Leymus racemosus. Significant homology was found between the Lt1 family and numerous repetitive sequences from Poaceae species, indicating that the Lt1 is an ancient family of tandemly repeated sequences in grasses. Key words: lymegrass, Leymus triticoides, [C.sub.0]t-1 DNA, satellite sequences, chromosomal mapping, subtelomeric heterochromatin. Resume : Le genre Leymus (elymes) comprend environ 30 especes de graminees perennes polyploides et de zone temperee au sein de la tribu des triticees (famine des poacees). Des etudes anterieures ont revele une grande diversity au sein du genome des Leymus d'ou l'interet de cette etude visant a isoler de nouvelles sequences repetees pouvant servir a distinguer les especes de Leymus et a elucider leur relations genomiques. Une banque de clones plasmidiques preparee a partir d'ADN [C.sub.0]t-1 a ete produite avec l'ADN genomique de fespece americaine tetraploide Leymus triticoides. Une famine de sequences d'ADN satellite tres grandement repetees, nommee Lt1, a ete isolee au sein de cette banque. La famine Lt1 est constituee d'unites SacI de 380 pb organisees en suites d'elements repetes en tandem. Une sous-famine caracterisee par un element repete MspI de 120 pb a ete decouverte au sein de cette famine, ce qui suggere que la methylation des cytosines pourrait avoir joue un role important dans fevolution de cet ADN satellite. Le satellite Lt1 a ete localise au sein des blocs heterochromatiques subtelomeriques des chromosomes du L. triticoides, lesquels sont presents sur tous les chromosomes et souvent sur les deux bras. Les sequences Lt1 sont abondantes chez le L. triticoides, alors qu'elles sont absentes de fespece tres voisine Leymus racemosus. Une homologie significative a ete trouvee entre la famine Lt1 et plusieurs sequences repetees chez d'autres poacees, ce qui indique que Lt1 serait une famine ancienne de sequences repetees en tandem chez les graminees. Mots-cles : elymes, Leymus triticoides, ADN [C.sub.0]t-1, sequences d'ADN satellite, cartographie chromosomique, heterochromatine subtelomerique., Introduction The genus Leymus (lymegrass) comprises about 30 perennial grass species in the tribe Triticeae, family Poaceae (Dewey 1984; Love 1984). Characteristic features of Leymus include stiff leaves, leaf blades [...]

Transnational cooperation is a common strategy for addressing research and development (R&D) issues resulting from similar challenges that cut across administrative borders. Value chains for food and drinks are complex, and transdisciplinary work is recognised as a method for solving complex issues. The Northern Cereals project ran from 2015 to 2018, and its goal was to increase cereal production and the value of grain products in four regions in the Northern Periphery programme area. The project included both R&D, but the main emphasis was on development, and was carried out by transdisciplinary cooperation between R&D partners and small and medium-sized enterprises (SMEs). By reviewing the project’s methods, outcomes and composition, we discuss if a framework of transnational and transdisciplinary cooperation can help to develop the value chain from local barley to beer. We found that transnational cooperation was achieved successfully, that stakeholder involvement was crucial, but that academic disciplines such as marketing and innovation could have been included. In addition, we recognised that much work remains to further increase cereal production and the use of local grain in the Northern Periphery region, but believe that this project has laid a good foundation for further progress.

Objective: Sidalcea is a genus of flowering plants restricted to the west coast of North America, commonly known as checkermallows. Remarkably, of the ~ 30 recognized species, 16 are of conservation concern (vulnerable, imperilled or critically imperilled). To facilitate biological studies in this genus, and in the wider Malvaceae, we have sequenced the whole plastid genome of Sidalcea hendersonii. This will allow us both to check those regions already developed as general Malvaceae markers in a previous study, and to search for new regions., Results: By comparing the Sidalcea genome to that of Althaea, we have identified a hypervariable circa 1 kb region in the short single copy region. This region shows promise for examining phylogeographic pattern, hybridization and haplotype diversity. Remarkably, considering the conservation of plastome architecture between Sidalcea and Althaea, the former has a 237 bp deletion in the otherwise highly conserved inverted repeat region. Newly designed primers provide a PCR assay to determine presence of this indel across the Malvaceae. Screening of previously designed chloroplast microsatellite markers indicates two markers with variation within S. hendersonii that would be useful in future population conservation genetics., (© 2023. The Author(s).)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin-probably Russian-of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus., Results: The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species ("core Trifolium") proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the "refractory clade" (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) and Trifolium subg. Trifolium (16.1 MYA)., Conclusions: We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.

Background and Aims: Cultivated flax (Linum usitatissimum) is known to have undergone a whole-genome duplication around 5-9 million years ago. The aim of this study was to investigate whether other whole-genome duplication events have occurred in the evolutionary history of cultivated flax. Knowledge of such whole-genome duplications will be important in understanding the biology and genomics of cultivated flax., Methods: Transcriptomes of 11 Linum species were sequenced using the Illumina platform. The short reads were assembled de novo and the DupPipe pipeline was used to look for signatures of polyploidy events from the age distribution of paralogues. In addition, phylogenies of all paralogues were assembled within an estimated age window of interest. These phylogenies were assessed for evidence of a paleopolyploidy event within the genus Linum., Key Results: A previously unknown paleopolyploidy event that occurred 20-40 million years ago was discovered and shown to be specific to a clade within Linum containing cultivated flax (L. usitatissimum) and other mainly blue-flowered species. The finding was supported by two lines of evidence. First, a significant change of slope (peak) was shown in the age distribution of paralogues that was phylogenetically restricted to, and ubiquitous in, this clade. Second, a large number of paralogue phylogenies were retrieved that are consistent with a polyploidy event occurring within that clade., Conclusions: The results show the utility of multi-species transcriptomics for detecting whole-genome duplication events and demonstrate that that multiple rounds of polyploidy have been important in shaping the evolutionary history of flax. Understanding and characterizing these whole-genome duplication events will be important for future Linum research.

Background: Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species., Results: (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome., Conclusions: (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a "fingerprint" to identify and characterize cacao accessions.

Premise of Study: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the plastid and ribosomal DNA, we call our approach ultra-barcoding (UBC)., Methods: We used high-throughput next-generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao., Key Results: All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA., Conclusions: Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.

The oral and dental health of patients with Parkinson's disease (PD) has not been well documented and the findings are conflicting. Patients with PD were invited to take part in a clinical and radiographic examination together with a comparison control group of persons who were a spouse or family member. Subjects (n = 67) and controls (n = 55) were examined and compared. Subjects with PD had more missing teeth, caries, dental plaque, and poorer periodontal health. Counts of cariogenic bacteria in saliva were significantly higher for subjects with PD. They did not consume more sweets or sugar, did not brush less frequently, used dental floss more than controls, and visited the dentist at least as often. Salivary flow levels were comparable between subjects with PD and controls. The lack of muscular control may explain the poorer oral health of patients with PD. Dentists and patients with PD may be reluctant to embark on complex dental procedures, and this may explain the increased number of missing teeth in persons with PD in this study.

Objective: We have previously shown that in the treatment of mild to moderate hypertension little is gained by increasing the dose of hydrochlorothiazide (HCT) over 12.5 mg when combined with an ACE-inhibitor. An increase in dosing was associated with more numerous side effects. The present study was designed to explore the relative efficacy of 12.5 and 6.25 mg of HCT in combination with captopril (C)., Material and Methods: For the study 25 patients with mild hypertension were recruited. Their mean age was 63 years (SD +/- 13 years). After a four week wash-out period and a dose finding phase of eight weeks, eight patients were stabilised at a diastolic pressure of <95 mmHg on C 50 mg + HCT 12.5 mg and 17 on C 25 mg + HCT 12.5 mg. These doses of C were continued throughout the study. The patients were then divided in two groups, receiving 12.5 mg or 6.25 mg of HCT for four weeks. The groups were then crossed over and treated for a further four week period. Finally, placebo was given for HCT for four weeks., Results: Although the mean supine blood pressure was lower on HCT 6.25 mg than placebo by 5/3 mmHg this difference was not significant. The pressure fall on HCT 12.5 mg in comparison with placebo was significant (9/7 mmHg, p<0.02) and the supine systolic blood pressure was similarly significantly lower on HCT 12.5 mg than 6.25 mg (p<0.02). The mean serum-K was significantly reduced by HCT 12.5 mg but only two patients had values below 3.5 mmol/1 and none below 3.0 mmol/1. No change was observed in serum creatinine values. No significant increase was reported in side effects on HCT + C in comparison with placebo + C., Conclusion: This and our previous studies suggest an optimal dose of HCT of approximately 12.5 mg. A dose of 6.25 mg may not be without an antihypertensive effect. However, such an effect is likely to be modest.