Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2023
Abstract
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Authors
Claire CoutrisAbstract
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Authors
Tomás Brůna Rishi Aryal Olga Dudchenko Daniel James Sargent Daniel Mead Matteo Buti Andrea Cavallini Timo Hytönen Javier Andrés Melanie Pham David Weisz Flavia Mascagni Gabriele Usai Lucia Natali Nahla Bassil Gina E. Fernandez Alexandre Lomsadze Mitchell Armour Bode Olukolu Thomas Poorten Caitlin Britton Jahn Davik Hamid Ashrafi Erez Lieberman Aiden Mark Borodovsky Margaret WorthingtonAbstract
Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosomelength assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298Mb, of which 270Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Abstract
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Abstract
Parametric modeling of downwelling longwave irradiance under all-sky conditions (LW↓) typically involves “correcting” a clear- (or non-overcast) sky model estimate using solar-irradiance-based proxies of cloud cover in lieu of actual cloud cover given uncertainties and measurement challenges of the latter. While such approaches are deemed sound, their application in time and space is inherently limited. We report on a correction model free of solar irradiance-derived cloud proxies that is applicable at the true daily (24 hr) and global scales. The new “cloud-free” correction model demonstrates superior performance in a range of environments relative to existing cloud-free modeling approaches and to corrections based on solar-derived cloudiness proxies. Literature-based performance benchmarking indicates a performance that is often comparable to—and in some cases superior to—performances yielded by conventional parametric modeling approaches employing locally or regionally calibrated parameters, as well as to performances of satellite-based algorithms.
Abstract
No abstract has been registered
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
Abstract
Light penetration plays a vital role in lakes and drinking water reservoirs, influencing fundamental processes such as primary production and thermal budgets. The Secchi depth (ZSD) and the compensation depth (ZCD) are commonly used measurements in this context. ZSD is determined through visual inspection using a Secchi disc, while ZCD represents the depth at which photosynthetic activity balances respiration and can be measured using a quantum irradiance sensor. Through in situ water-core samples from 23 lakes within a lake district in Southeastern Norway, we observed that DNOM exerts a diverse influence on these light irradiance measurements. If DNOM concentrations are reduced to half or a quarter of the current concentration, similar to what was measured during the 1980s, the median ZCD:ZSD ratios are estimated to have decreased by approximately 30 and 60% since then, respectively. Conversely, a plausible future climate-driven doubling or quadrupling of the present DNOM concentrations are estimated to further decrease the median ZCD:ZSD ratios in the lake district with approximately 10 and 25%, respectively. From this, the ZCD:ZSD ratios seem to have experienced a considerable long-term decline attributed to both climate change and the recovery from acid rain, and a further climate-driven decrease is expected.
Authors
Michelle Devlin Theo C. Prins Lisette Enserink Wera Leujak Birgit Heyden Philip Axe Hans Ruiter Anouk Blauw Eileen Bresnan Kate Collingridge David Devreker Liam Fernand Francisco Gomez Jakobsen Carolyn Graves Alain Lefebvre Herman-J. Lenhart Stiig Markager Marta Nogueira Garvan O’Donnell Hjalte Parner Eva Skarbøvik Morten D. Skogen Lars Sonesten Sonja M. Van Leeuwen Robert Wilkes Eleanor Dening Alejandro Iglesias-CamposAbstract
No abstract has been registered
Authors
Freya Ziegler Anita Sønsteby Agnieszka Masny Charles Underwood Lucas Munnes Vivien Rosenthal Sonia Osorio Björn UsadelAbstract
No abstract has been registered