| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
- Crous, P. W., et al.
(författare)
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Fusarium : more than a node or a foot-shaped basal cell
- 2021
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Ingår i: Studies in mycology. - : CENTRAALBUREAU SCHIMMELCULTURE. - 0166-0616 .- 1872-9797. ; :98
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Tidskriftsartikel (refereegranskat)abstract
- Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
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| 3. |
- Wang, K., et al.
(författare)
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Amended soils with weathered coal exhibited greater resistance to aggregate breakdown than those with biochar : From the viewpoint of soil internal forces
- 2024
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Ingår i: Soil & Tillage Research. - : Elsevier B.V.. - 0167-1987 .- 1879-3444. ; 244
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Tidskriftsartikel (refereegranskat)abstract
- Soil erosion is the first threat to soil functions. Reducing the soil aggregate breakdown strength is a key step to improve the soil's ability to resist rainfall splash erosion. Soil internal forces have been found to be the initial and important forces driving aggregate turnover. The application of exogenous organic materials can effectively improve soil aggregate stability and the resistance to rainfall erosion of agricultural soils. However, from the perspective of soil internal forces, information about the reduction effects of the exogenous organic materials application on soil aggregate breakdown is scarce, especially in comparing the effects of different materials. In this study, weathered coal and biochar were individually applied to loamy clay soil at rates of 0 %, 1 %, 2 %, and 3 % (w/w). Soil internal forces, aggregate breakdown strength, and splash erosion rate of different amended soils were then examined after four years. The results showed that compared with unamended soils (0 %), both weathered coal and biochar applications clearly increased the van der Waals attractive pressure and thus decreased the positive net pressure between soil particles. Additionally, these materials reduced soil aggregate breakdown strength and splash erosion rate. The application effects of the two materials were increased with their application rates. Under a lower electrolyte concentration in soil solution (0.0001 mol L−1), the aggregate breakdown strength in the soils amended with weathered coal was lower than that with biochar by 9.6 %, 23.2 %, and 17.7 % (when the diameter of broken aggregate was < 10 μm) and by 10.3 %, 20.8 %, and 17.5 % (when the diameter of broken aggregate was < 20 μm) at the 1 %, 2 %, and 3 % application rates, respectively (P < 0.05). Additionally, soils amended with weathered coal exhibited lower splash erosion rates compared to those amended with biochar, particularly at the higher application rate of 3 %. From the viewpoint of soil internal forces, weathered coal appears to be a suitable exogenous organic material for improving soil aggregate stability and anti-erosion ability during rainfall events. Our findings provide valuable insights into utilizing exogenous materials to improve soil resistance to rainfall splash erosion, assisting agricultural soil management in areas frequently affected by rainfall erosion.
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| 4. |
- Anderbrant, Olle, et al.
(författare)
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Attraction of Male Pine Sawflies, Diprion jingyuanensis, to Synthetic Pheromone Candidates: Synergism between Two Stereoisomers
- 2023
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Ingår i: Forests. - : MDPI. - 1999-4907. ; 14:6
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Tidskriftsartikel (refereegranskat)abstract
- The pine sawfly Diprion jingyuanensis Xiao and Zhang (Hymenoptera: Diprionidae) is a serious pest of Pinus tabulaeformis Carr. in the Shanxi, Gansu, and Inner Mongolia provinces in P. R. China. The sex pheromone of D. jingyuanensis was shown to be the propionate ester of 3,7-dimethyl-2-tridecanol. Virgin females contained an approximate 1:3 blend of the pheromone precursors erythro-(2S,3S,7R/S and 2R,3R,7R/S)-3,7-dimethyl-2-tridecanol and threo-(2S,3R,7R/S and 2R,3S,7R/S)-3,7-dimethyl-2-tridecanol, but the exact stereoisomers were not determined. Males responded the strongest to the propionate ester of the two threo-isomers, (2S,3R,7R) and (2S,3R,7S), in electroantennogram (EAG) recordings, followed by a significant EAG response to the (2S,3R,7R) propionate of diprionol (pheromone component of D. similis), whereas the remaining two isomers (2S,3S,7S and 2S,3S,7R) of the propionate ester of 3,7-dimethyl-2-tridecanol and the acetate of the (2S,3R,7R) isomer (one of the two pheromone components of D. pini) did not elicit any significant increase in antennal response. In the field, the strongly EAG-active (2S,3R,7R)-isomer alone was only weakly (but significantly) attractive to D. jingyuanensis males at 100 & mu;g, while the equally EAG- active (2S,3R,7S)-isomer alone at the same loading was 8-14 times more attractive than was the (2S,3R,7R)-isomer alone. Traps baited with the same amounts of the two threo-isomers ((2S,3R,7R) and (2S,3R,7S), 100 & mu;g + 100 & mu;g) caught significantly more males than did traps baited with other isomers, either of the two isomers alone or other proportions of the two isomers. Thus, the (2S,3R,7S)-isomer is considered as a strong and essential sex-attractant component for D. jingyuanensis males, whereas the (2S,3R,7R)-isomer is a weak but synergistic sex-attractant. This is one of the few examples of a pine sawfly responding significantly stronger to a binary blend of stereoisomers in a synergistic fashion than to a single stereoisomer alone.
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| 5. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 6. |
- Zhang, X., et al.
(författare)
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Greater mineral and aggregate protection for organic carbon in the soil amended by weathered coal than by biochar : Based on a 3-year field experiment
- 2023
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Ingår i: Geoderma. - : Elsevier B.V.. - 0016-7061 .- 1872-6259. ; 438
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Tidskriftsartikel (refereegranskat)abstract
- Soil carbon pool stability plays an important role in reaching carbon neutrality and mitigating global warming. Applying soil amendments is a practical strategy in agricultural production to improve soil environment. Weathered coal (WC) is an organic amendment that can be used to improve soil quality. However, the effects of WC application on soil organic carbon pool stability, and its differences from the effects of biochar (BC, a common amendment) application remains unclear. In this study, BC was selected as a comparison to further evaluate the potential of WC based on a 3-year field experiment, in which WC and BC were individually applied into a loamy clay soil at 0%, 1%, and 3% (w/w) rates. Soil organic carbon and its fractions (including particulate organic carbon and mineral-bound organic carbon), soil aggregate fractions and its stability, and the organic carbon content in aggregates were examined. The results showed that both WC and BC significantly increased soil total organic carbon, particulate and mineral-bound organic carbon (P < 0.05). The mineral-bound organic carbon content in WC treatment was significantly higher than that in BC treatment (by 32% under the 3% rate) (P < 0.05), whereas, there were no significant differences in soil total organic carbon content. Both WC and BC increased the soil organic carbon content in all aggregate fractions. While only the WC improved the soil aggregate stability, and which was 15% (under 1% rate) and 28% (under 3% rate) higher in WC treatments than in BC treatments (P < 0.05). The proportion of mineral-bound organic carbon to soil total organic carbon content and the soil aggregate stability were obviously related the soil C/N, and the WC treatments had a higher proportion of mineral-bound organic carbon and soil aggregate stability than BC treatments under the same soil C/N. The results indicated that the application of WC may be more effective than BC in increasing mineral and aggregate protection for soil organic carbon and thus improving soil carbon pool stability. Additionally, the purchase cost of WC was clearly lower than that of BC. Combined with the low cost and the benefits in soil structure and carbon pool stability, the application of WC appeared to have advantages over BC. Our findings provide robust evidence that WC is more effective than BC in improving soil carbon pool stability.
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| 7. |
- Abramoff, Rose Z., et al.
(författare)
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How much carbon can be added to soil by sorption?
- 2021
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Ingår i: Biogeochemistry. - : Springer Nature. - 0168-2563 .- 1573-515X. ; 152:2-3, s. 127-142
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Tidskriftsartikel (refereegranskat)abstract
- Quantifying the upper limit of stable soil carbon storage is essential for guiding policies to increase soil carbon storage. One pool of carbon considered particularly stable across climate zones and soil types is formed when dissolved organic carbon sorbs to minerals. We quantified, for the first time, the potential of mineral soils to sorb additional dissolved organic carbon (DOC) for six soil orders. We compiled 402 laboratory sorption experiments to estimate the additional DOC sorption potential, that is the potential of excess DOC sorption in addition to the existing background level already sorbed in each soil sample. We estimated this potential using gridded climate and soil geochemical variables within a machine learning model. We find that mid- and low-latitude soils and subsoils have a greater capacity to store DOC by sorption compared to high-latitude soils and topsoils. The global additional DOC sorption potential for six soil orders is estimated to be 107 ± 13 Pg C to 1 m depth. If this potential was realized, it would represent a 7% increase in the existing total carbon stock.
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| 8. |
- Awasthi, S K, et al.
(författare)
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Multi-criteria research lines on livestock manure biorefinery development towards a circular economy : From the perspective of a life cycle assessment and business models strategies
- 2022
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Ingår i: Journal of Cleaner Production. - : Elsevier. - 0959-6526 .- 1879-1786. ; 341
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Tidskriftsartikel (refereegranskat)abstract
- Livestock manure (LSM) is a profitable waste if handled sensibly, but simultaneously it imposes several environmental and health impacts if managed improperly. Several approaches have been adopted globally to cartel the problem associated with LSM management and recovery of value-added products, still, technological innovation needs further upgradation in consideration with the environment, energy, and economy. This review delivered a vibrant portrait of manure management, which includes, bioenergy generation and resource recovery strategies, their current scenario, opportunities, challenges, and prospects for future researches along with global regulations and policies. Several bioenergy generation and nutrient recoveries technologies have been discussed in details, still, the major glitches allied with these technologies are its high establishment costs, operational costs, manure assortment, and digestate handling. This review also discussed the techno-economic assessment (TEA) and life cycle assessment (LCA) of LSM management operation in the context of their economical and environmental sustainability. Still, extensive researches needed to build an efficient manure management framework to advance the integrated bioenergy production, nutrients recycling, and digestate utilization with least environmental impacts and maximal economical gain, which has critically discussed in the current review.
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| 9. |
- Chen, Z, et al.
(författare)
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Importance of heterotrophic nitrification and dissimilatory nitrate reduction to ammonium in a cropland soil: Evidences from a 15N tracing study to literature synthesis
- 2015
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 91, s. 65-75
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Tidskriftsartikel (refereegranskat)abstract
- Future climate change is predicted to influence soil moisture regime, a key factor regulating soil nitrogen (N) cycling. To elucidate how soil moisture affects gross N transformation in a cultivated black soil, a 15N tracing study was conducted at 30%, 50% and 70% water-filled pore space (WFPS). While gross mineralization rate of recalcitrant organic N (Nrec) increased from 0.56 to 2.47 mg N kg−1 d−1, the rate of labile organic N mineralization declined from 4.23 to 2.41 mg N kg−1 d−1 with a WFPS increase from 30% to 70%. Similar to total mineralization, no distinct moisture effect was found on total immobilization of ammonium, which primarily entered the Nrec pool. Nitrate (NO3−) was mainly produced via autotrophic nitrification, which was significantly stimulated by increasing WFPS. Unexpectedly, heterotrophic nitrification was observed, with the highest rate of 1.06 mg N kg−1 d−1 at 30% WFPS, contributing 31.8% to total NO3− production, and decreased with WFPS. Dissimilatory nitrate reduction to ammonium (DNRA) increased from near zero (30% WFPS) to 0.26 mg N kg−1 d−1 (70% WFPS), amounting to 16.7–92.9% of NO3− consumption. A literature synthetic analysis from global multiple ecosystems showed that the rates of heterotrophic nitrification and DNRA in test soil were comparative to the forest and grassland ecosystems, and that heterotrophic nitrification was positively correlated with precipitation, soil organic carbon (SOC) and C/N, but negatively with pH and bulk density, while DNRA showed positive relationships with precipitation, clay, SOC, C/NO3− and WFPS. We suggested that low pH and bulk density and high SOC and C/N in test soil might favor heterotrophic nitrification, and that C and NO3− availability together with anaerobic condition were crucial for DNRA. Overall, our study highlights the role of moisture in regulating gross N turnover and the importance of heterotrophic nitrification for NO3− production under low moisture and DNRA for NO3− retention under high moisture in cropland.
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| 10. |
- Meadows, Jennifer, et al.
(författare)
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Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 x data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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