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420 results for “novel associations”
Data from: Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution
Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice-planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy-rice specific novel SNPs by genome-wide comparison between DNA sequences of weedy and cultivated rice, in addition to PCR fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice-planting regions. The highest frequency (~57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (~29%) was detected in weedy rice populations from Northeast China where rice farming has a relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.
Fig. 1 in Stephanopachys conicolaFisher (Coleoptera: Bostrichidae) Feeding on Decaying Western Juniper (Juniperus occidentalisHooker) Berries: A Novel Association for Bostrichidae
Fig. 1. Stephanopachys conicola, lateral and dorsal views.
Figure 1. Clubiona filicata Cambridge O in A novel host association of Idris Förster (Hymenoptera: Scelionidae) with description of a new species from India
Figure 1. Clubiona filicata Cambridge O. Pickard (adult female).
Figure 1 from: Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S (2024) Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. In: Wijayawardene N, Karunarathna S, Fan X-L, Li Q-R (Eds) Taxonomy and secondary metabolites of wood-associated fungi. MycoKeys 104: 9-50. https://doi.org/10.3897/mycokeys.104.112149
Figure 1 Phylogram of the best-scoring ML consensus tree of taxa in Bambusicolaceae and Occultibambusaceae. The new isolate is indicated in blue. Isolates from type materials are in bold. The ML ultrafast bootstrap and Bayesian PP values greater than 60% and 0.90 are shown at the nodes.
Figure 2 from: Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S (2024) Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. In: Wijayawardene N, Karunarathna S, Fan X-L, Li Q-R (Eds) Taxonomy and secondary metabolites of wood-associated fungi. MycoKeys 104: 9-50. https://doi.org/10.3897/mycokeys.104.112149
Figure 2 Phylogram of the best-scoring ML consensus tree of Trichobotrys species in Dictyosporiaceae and closely-related families viz. Didymosphaeriaceae, Lentitheciaceae, Morosphaeriaceae, Sulcatisporaceae and Trematosphaeriaceae. The new isolate is indicated in blue. Isolates from type materials are in bold. The ML ultrafast bootstrap and Bayesian PP values greater than 70% and 0.95 are shown at the nodes.
Figure 5 from: Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S (2024) Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. In: Wijayawardene N, Karunarathna S, Fan X-L, Li Q-R (Eds) Taxonomy and secondary metabolites of wood-associated fungi. MycoKeys 104: 9-50. https://doi.org/10.3897/mycokeys.104.112149
Figure 5 Trichobotrys sinensis (KUN-HKAS 129041, holotype) A, B the appearance of colonies on the host surface C mycelium D–H conidiophores bearing conidiogenous cells and conidia I conidia in a short acropetal chain J–N conidia O culture characteristics on PDAP conidioma forming on PDA after eight weeks Q pycnidial wall R–T conidiogenous cells (note: T = stained in Congo red) U conidia. Scale bars: 100 μm (P); 50 μm (C); 10 μm (D–H, Q–U); 5 μm (J–N).
Figure 3 from: Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S (2024) Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. In: Wijayawardene N, Karunarathna S, Fan X-L, Li Q-R (Eds) Taxonomy and secondary metabolites of wood-associated fungi. MycoKeys 104: 9-50. https://doi.org/10.3897/mycokeys.104.112149
Figure 3 Phylogram of the best-scoring ML consensus tree of taxa in Periconiaceae and the closely-related families Lentitheciaceae and Massarinaceae. The new isolate is indicated in blue. Isolates from type materials are in bold. The ML ultrafast bootstrap and Bayesian PP values greater than 50% and 0.95 are shown at the nodes.
Figure 4 from: Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S (2024) Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. In: Wijayawardene N, Karunarathna S, Fan X-L, Li Q-R (Eds) Taxonomy and secondary metabolites of wood-associated fungi. MycoKeys 104: 9-50. https://doi.org/10.3897/mycokeys.104.112149
Figure 4 Bambusicola hongheensis (KUN-HKAS 129042, holotype) A the appearance of ascomata on the host surface B vertical section of an ascoma C, D peridia E pseudoparaphyses F, G asci embedded in pseudoparaphyses H–K ascospores L, M ascospores stained in India Ink show a thin mucilaginous sheath surrounding ascospores. Scale bars: 100 μm (B); 20 μm (C–G); 10 μm (H–M).
Figure 6 from: Phookamsak R, Hongsanan S, Bhat DJ, Wanasinghe DN, Promputtha I, Suwannarach N, Kumla J, Xie N, Dawoud TM, Mortimer PE, Xu J, Lumyong S (2024) Exploring ascomycete diversity in Yunnan II: Introducing three novel species in the suborder Massarineae (Dothideomycetes, Pleosporales) from fern and grasses. In: Wijayawardene N, Karunarathna S, Fan X-L, Li Q-R (Eds) Taxonomy and secondary metabolites of wood-associated fungi. MycoKeys 104: 9-50. https://doi.org/10.3897/mycokeys.104.112149
Figure 6 Periconia kunmingensis (KUN-HKAS102239, holotype) A, B the appearance of fungal colonies on host substrate C–E conidiophores F, G closed-up conidiophores with spherical heads H, I conidiogenous cells bearing conidia J conidia catenate in acropetal short chain K–P conidia. Scale bars: 500 µm (A, B); 50 µm (C–E); 20 µm (F, G); 10 µm (J); 5 µm (H, I, K–P).
Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison
<p>Petal size determines the value of ornamental plants, and thus their economic worth. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes regulating petal size in rapeseed (<i>Brassica napus</i>), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 17 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with extreme differences in petal size identified 11 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, <i>BnaA05</i><i>.</i><i>RAP2.2</i> homologous to <i>RAP2.2</i> in rapeseed may be a critical gene negatively influencing petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two extreme accessions were determined mainly by cell number differences. Finally, we propose a preliminary model for the control of petal size in rapeseed. Our results provide insights into the genetic mechanisms regulating petal size, and also lay the foundation for a better understanding of petal development in plants.</p>
Dataset for: A novel hydrophobically associating water-soluble polymer utilized as constant rheology agent for cement slurry
During the process of well cementing in deepwater, the cement slurry experiences a wide range of temperature variation from low temperature at seabed to high temperature in downhole. The elevated temperature affects the rheology of cement slurry. The change of rheology of cement slurry could influence the safety of cementing operation. The aim of this paper is to develop a new kind of hydrophobically associating water-soluble polymer (KWHL-1) as an additive to prepare a constant rheology oil well cement slurry, which can be used at temperature range from 4℃ to 90℃. The acrylamide, 2-acrylamide-2-methylpropionic acid and stearyl methylacrylate were applied to synthesize the KWHL-1 by the inverse microemulsion polymerization. Test results indicate that the critical association temperature of KWHL-1 is 45℃. The critical association temperature is independent with KWHL-1 concentration, salt concentration and alkalinity of solution. When the temperature is below 45℃, KWHL-1 shows little influence on the viscosity of solution. When the temperature is above 45℃, the KWHL-1 forms spatial network structure by intermolecular hydrophobic association, and thus increases the viscosity of solution significantly. The KWHL-1 also displays good thermal stability and excellent salt and alkali resistance properties. In addition, the KWHL-1 shows nearly no negative influence on the basic properties of cement slurry, which indicates that the KWHL-1 can be used as a constant rheology agent to prepare a cement slurry with constant rheology in the temperature range of 4 to 90℃.
A novel genome-wide association approach reveals wheat pathogen genes involved in host specialization
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Figure 5 from: Norphanphoun C, Raspé O, Jeewon R, Wen T-C, Hyde KD (2018) Morphological and phylogenetic characterisation of novel Cytospora species associated with mangroves. MycoKeys 38: 93-120. https://doi.org/10.3897/mycokeys.38.28011
Figure 5 Cytosporaxylocarpi (MFLU 17-0708, holotype). aXylocarpusgranatumb Branch of XylocarpusgranatumcAscostromata on host substrate d Surface of ascomata e Transverse sections through ascostroma to show distribution of locules f, g Longitudinal sections through ascostroma to show distribution of locules hPeridiumi–l, n Asci m, oAscosporesp Germinating spore q, r Colonies on MEA (q-from above, r-below) s Transverse sections through conidioma to show distribution of locules t Longitudinal sections through conidioma to show distribution of locules u, v Conidiogenous cells with attached conidia w Mature conidia. Scale bars: c = 2000 µm, d–f = 500 µm, g = 200 µm, h = 20 µm, i, p = 10 µm, j–o, u–w = 5 µm, s, t = 400 µm.
Figure 3 from: Norphanphoun C, Raspé O, Jeewon R, Wen T-C, Hyde KD (2018) Morphological and phylogenetic characterisation of novel Cytospora species associated with mangroves. MycoKeys 38: 93-120. https://doi.org/10.3897/mycokeys.38.28011
Figure 3 Cytosporalumnitzericola (MFLUCC 17-0508, from culture). a Mangrove collecting site b, cLumnitzeraracemosa in mangroves forest d, e Colonies on MEA after 6 days (left) and 30 days (right) (d-from above, e-from below) f, gConidiomata produced on MEAh, l Transverse sections of conidioma i, j, n Conidiogenous cells with attached conidia k, mConidia. Scale bars: f = 1000 µm, g, h = 500 µm, i, j = 10 µm, k = 5 µm.
Figure 2 from: Norphanphoun C, Raspé O, Jeewon R, Wen T-C, Hyde KD (2018) Morphological and phylogenetic characterisation of novel Cytospora species associated with mangroves. MycoKeys 38: 93-120. https://doi.org/10.3897/mycokeys.38.28011
Figure 2 Maximum parsimony phylogenetic tree inferred from ITS1 and ITS2 sequence data. Maximum parsimony and maximum likelihood bootstrap values ≥50%, Bayesian posterior probabilities ≥0.90 (MPBS/MLBS/BIPP) are given at the nodes. The species obtained in this study are in blue font. Ex-type taxa from other studies are in black bold.
Figure 1 from: Norphanphoun C, Raspé O, Jeewon R, Wen T-C, Hyde KD (2018) Morphological and phylogenetic characterisation of novel Cytospora species associated with mangroves. MycoKeys 38: 93-120. https://doi.org/10.3897/mycokeys.38.28011
Figure 1 Phylogram generated from maximum parsimony analyses based on analysis of combined ITS, LSU, ACT and RPB2 sequence data. The tree is rooted to Diaportheeres (AFTOL-ID 935). Maximum parsimony and maximum likelihood bootstrap values ≥50%, Bayesian posterior probabilities ≥0.90 (MPBS/MLBS/PP) are given at the nodes. The species obtained in this study are in blue font. Ex-type taxa from other studies are in black bold.
Figure 4 from: Norphanphoun C, Raspé O, Jeewon R, Wen T-C, Hyde KD (2018) Morphological and phylogenetic characterisation of novel Cytospora species associated with mangroves. MycoKeys 38: 93-120. https://doi.org/10.3897/mycokeys.38.28011
Figure 4 Cytosporathailandica (MFLU 17-0709, holotype). aXylocarpusmoluccensisb Branch of XylocarpusmoluccensiscAscostromata on host substrate d, e Surface of ascomata f Transverse sections through ascostroma to show distribution of locules g–h Longitudinal sections through ascostroma to show distribution of locules iPeridiumj Ostiolar neck ka–kd, n Asci l, m Apical ring oa–ofAscosporesp Surface of conidioma q Transverse sections through conidioma to show distribution of locules r, s Longitudinal sections through conidioma to show distribution of locules tPeridiumu Ostiolar neck va–vc, w Conidiogenous cells with attached conidia x, yConidiaza, zb Colonies on MEA (za-from above, zb-from below). Scale bars: d = 1000 µm, e–g = 400 µm, h, j, p–s = 200 µm, i, u = 100 µm, ka–kd, n = 10 µm, l, m = 2 µm, oa–of, va–vc, w = 5 µm, t = 50 µm, x, y = 4 µm.
Figure 4 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090
Figure 4 Infected host organs and spore images of R.xanthophloeae (A–H), R.natalensis (I), R. evansii (J) and R.macowaniana (K) A Infected individual of V.xanthophloea. Leaves were prematurely shed in comparison with uninfected trees B Telia on leaflets of V.xanthophloeaC SEM of an aeciospore showing scattered germpores D SEM of an urediniospore E Urediniospores seen in LM F SEM view of a teliospore of R.xanthophloeae. The arrows indicate irregularly arranged verrucose ornamentations G Telium of R.xanthophloeae seen in SEM H LM view of a teliospore. The arrow indicates irregularly arranged verrucose ornamentations I Teliospores of R.natalensis with long pedicels J SEM picture of median section of a teliospore of R.evansii. Arrows indicate 2-celled probasidial cells K LM picture of teliospores of R.macowaniana. Scale bars: 1 mm (B), 4 μm (C), 2 μm (D), 20 μm (E), 20 μm (F–H, J–K), 40 μm (I).
Figure 3 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090
Figure 3 Radarchart of mean values of the morphological investigations of teliospore characteristics of Raveneliamacowaniana originated from Vachelliakarroo (red), V.natalitia (green) and R.xanthophloeae on V.xanthophloea (blue). Numbers on y-axis represent the respective minimum and maximum values. This radarchart reveals the morphological differences between R.macowaniana and R.xanthophloeae.
Figure 1 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090
Figure 1 Phylogenetic reconstruction of Ravenelia species on different Vachellia hosts A Maximum likelihood tree with 1000 bootstrap repeats based on combined nrITS and LSU rDNA sequence data. Bootstrap values below 75 are not shown. Three highly supported groups represent R.evansii, R.macowaniana and R.xanthophloeae sp. nov., respectively. Specimens that originated from formerly unreported host species are highlighted in bold B Parsimony network analysis based on the same dataset as in the ML-analysis. Each line represents one base substitution while small circles represent intermediate but missing sequences. Numbers next to lines indicate the positions of the substitutions in the alignment. Sequences in rectangular boxes were inferred as ancestral by this analysis.
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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.