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Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
<p><span>The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen <em>Verticillium dahliae</em>,<em> </em>known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for <em>V. dahliae </em>are also present in other <em>Verticillium</em> species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the <em>Verticillium</em> genus.</span></p>
Figure 5 in Three new genera of Protandrenini bees from South America (Hymenoptera, Apidae, Andreninae)
Figure 5 Cisanthrena perforata Ramos & Melo new species, male paratype. A, apex of metasoma, showing the T7, in postero-dorsal view. B, S6 in ventral view. C, S7 in ventral view. D, S8 in ventral view. E, genitalia in lateral view. F, genitalia in ventral view. Scale bar 0.2 mm.
Figure 4 Cisanthrena perforata Ramos & Melo new species. A in Three new genera of Protandrenini bees from South America (Hymenoptera, Apidae, Andreninae)
Figure 4 Cisanthrena perforata Ramos & Melo new species. A, head of female (holotype) in frontal view. B, female (holotype) in lateral view. C, head of male (paratype) in frontal view. D, male (paratype) in dorsal view. Scale bar: 1.0 mm.
Figure 1 in Three new genera of Protandrenini bees from South America (Hymenoptera, Apidae, Andreninae)
Figure 1 Austellurgus avulsus (Ramos & Melo, 2006), paratypes. A, head of female in frontal view. B, female in lateral view. C, labrum and mandible of female in frontal view. D, head of male in frontal view. E, male in lateral view. F, labrum and mandible of male in frontal view. G, mesosoma of male in dorsal view. H, metasoma of female in dorsal view. I, apex of female metasoma, showing the pygidial plate. Scale bar: 0.5 mm.
Figure 2 in Three new genera of Protandrenini bees from South America (Hymenoptera, Apidae, Andreninae)
Figure 2 Luisanthrena ruzae Ramos & Melo new species, paratypes. A, head of female in frontal view. B, female in dorsal view. C, head of male in frontal view. D, male in lateral view. Scale bar: 0.5 mm.
263 MAG annotations for three nested metagenomic studies describe crop-shrub-microbe interactions in an agroecology system in the Sahel
<p>The Sahel region of West Africa is a vulnerable eco-region, where climate change induced drought and a rapidly growing population pose serious threats to food security and contribute to soil degradation. Local and biologically based systems are necessary to maintain crop yields and soil health, and intercropping with native woody shrubs Guiera senegalensis has been discovered as a solution. We have previously shown that soil microbial communities are significantly altered by the presence of shrubs, and that these organisms may have plant growth promoting properties. Here, we augment those data with metagenomic and metatranscriptomic data across three nested experiments: a landscape scale experiment across a rainfall and soil type gradient, a long-term experimental site, and a growth chamber simulated drought experiment. We recovered 263 95% ANI dereplicated metagenome-assembled genomes (MAGs) of medium and high quality to evaluate their relative enrichment and what their encoded metabolisms reveal about mechanisms of microbiome millet support. These data contribute to our understanding of the role of the microbial community crop drought resilience in the Sahel and in semi-arid cropping systems globally. Here we present the DRAM annotations of each MAG, all associated metadata, viral genes and vOTUs from the Optimized Shrub Intercropping Study (OSS), and eukaryotic contigs from the OSS</p>
Figs 1-5 in Three new rotundabaloghid mites (Acari: Uropodina) from Hong Kong
Figs 1-5. Angulobaloghia staryi sp. nov., female holotype. (1) Body in dorsal view. (2) Setae and ornamentation in central area of dorsal shield. (3) Setae and ornamentation in lateral part of dorsal shield. (4) Body in ventral view. (5) Ventral setae.
Figs 21-25 in Three new rotundabaloghid mites (Acari: Uropodina) from Hong Kong
Figs 21-25. Depressorotunda (Depressorotunda) taurina sp. nov., female holotype. (21) Body in dorsal view. (22) Setae and ornamentation in central area of dorsal shield. (23) Setae and ornamentation in lateral part of dorsal shield. (24) Body in ventral view. (25) Intercoxal area and ventral cavity in ventral view.
Figs 17-20 in Three new rotundabaloghid mites (Acari: Uropodina) from Hong Kong
Figs 17-20. Rotundabaloghia (Rotundabaloghia) hongkongensis sp. nov., female holotype. (17) Ventral view of leg I. (18) Ventral view of leg II. (19) Ventral view of leg III. (20) Ventral view of leg IV.
Figs 6-11 in Three new rotundabaloghid mites (Acari: Uropodina) from Hong Kong
Figs 6-11. Angulobaloghia staryi sp. nov., female holotype (6-10) and male paratype (11). (6) Ventral view of gnathosoma, tritosternum and coxae I. (7) Ventral view of leg I. (8) Ventral view of leg II. (9) Ventral view of leg III. (10) Ventral view of leg IV. (11) Ventral view of intercoxal area of male.
Figs 12-16 in Three new rotundabaloghid mites (Acari: Uropodina) from Hong Kong
Figs 12-16. Rotundabaloghia (Rotundabaloghia) hongkongensis sp. nov., female holotype (12-15) and male paratype (16). (12) Body in dorsal view. (13) Dorsal setae and ornamentation. (14) Ventral view of body. (15) Ventral view of gnathosoma, tritosternum and coxae I. (16) Ventral view of intercoxal area of male.
Figs 26-29 in Three new rotundabaloghid mites (Acari: Uropodina) from Hong Kong
Figs 26-29. Depressorotunda (Depressorotunda) taurina sp. nov., female holotype. (26) Ventral view of leg I and gnathosoma. (27) Ventral view of leg II. (28) Ventral view of leg III. (29) Ventral view of leg IV.
Figure 10 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 10: PCA biplot of environmental parameters and abundance of microarthropods with month as grouping factor. sav ctrl: savanna; mb: maize bare; mbnpk: maize with chemical NPK fertilizer; mmdom: maize with dead organic matter.
Figure 9 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 9. PCA biplot of environmental parameters and abundance of microarthropods with treatment as grouping factor. sav ctrl: savanna, mb: maize bare, mbnpk: maize with chemical NPK fertilizer, mmdom: maize with dead organic matter.
Figure 8 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 8. Oribatida and Gamasina abundance (tsd. ind./m2) in plots (mb: maize bare, mmdom: maize with DOM). Abundances being significantly different from each other are marked by different letters for each microarthropod group (Wilcoxon signed rank test [p ˂ 0.05]). Error bars = standard error.
Figure 7 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 7. Collembola, Oribatida and Gamasina abundance (tsd. ind./m2) in plots (mb: maize bare, mbnpk: maize with chemical NPK). Abundances being significantly different from each other are marked by different letters (Wilcoxon signed rank test [p ˂ 0.05]). Error bars = standard error.
Figure 6 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 6. Effect of Maize cultivation on Collembola, Oribatida and Gamasina in control plots (sav ctrl: savanna, mb: maize bare). Abundances being significantly different from each other are marked by different letters for each microarthropod group (Wilcoxon signedrank test [p ˂ 0.05]). Error bars = standard error.
Figure 5 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 5. Temporal variation of Collembola, Oribatida and Gamasina abundance (tsd. ind./m2) in savanna and experimental field in (A) 2017 and (B) 2018. Abundance being significantly different from each other in time per treatment are marked by different letters for each microarthropod group (Wilcoxon signed-rank test [p ˂ 0.05]). Months not sampled are marked by asterisks. Error bars = standard error. sav ctrl: savanna, mb: maize bare, mbnpk: maize with chemical NPK fertilizer, mmdom: maize with dry organic matter (DOM).
Figure 2 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 2. Completely randomized block design of the experimental field; experimental field before sowing (A: 08/05/17) and with maize crop (B: 28/06/17); sav ctrl: savanna untreated (outside). mb(1): maize bare = maize plot without mulch or NPK fertilizer; mbnpk(2): maize bare with NPK = Maize plot treated with NPK fertilizer only and mmdom(3): maize mulch = maize plot treated with mulch only.
Figure 1 in Effect of three different land use types on the temporal dynamics of microarthropod abundance in the high Guinean savanna of Ngaoundéré (Adamawa, Cameroon)
Figure 1. Weather data for the Ngaoundéré area, Jan. to Dec. 2017 and 2018, provided by Ngaoundéré airport meteorological station; t: temperature, p: precipitation, h: relative humidity; h: averages per month; p: sum per month.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.