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Fig. 3 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 3. Hierarchical cluster analysis (represented by a heat-map) of amino acids content in leaves of potato allo- and autotetraploids and cultivated varieties. Dendrograms were constructed by UPGMA clustering method for 18 amino acids and 10 lines: diploid S. kurtzianum parental line (2xPL), diploid S. tuberosum x S. kurtzianum parental interspecific hybrid (2xPIH), three autotetraploids (4xAuL1, 4xAuL2 and 4xAuL3), two allotetraploids (4xAL2 and 4xAL4) and three cultivated varieties (4xCalen, 4xInnovator and 4xPampeana).
Fig. 1 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 1. Fold change of compounds content in allotetraploids (a) and autotetraploids (b) relative to their respective diploid parental line. Fold change is expressed as log10(Tetraploid/Diploid). Horizontal lines are the average of the absolute logFC for each evaluated line, letters denote differences by Duncan's multiple range test (P <0.05).
Tracking the ancestry of known and 'ghost' homeologous subgenomes in model grass Brachypodium polyploids
<p>Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when genome sequences of known progenitors are unavailable. Existing subgenome identification methods cannot adequately infer the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus <i>Brachypodium,</i> which is a model genus for temperate cereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenome detection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic subgenome detection pipeline was validated in <i>Triticum</i> allopolyploids, which have known progenitor genomes, and was used to infer the identities of three subgenomes derived from extant diploid species and four subgenomes derived from unknown diploid progenitors (ghost subgenomes) in six <i>Brachypodium</i> polyploids (<i>B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestre, and B. hybridum</i>), of which five contain undescribed homeologous subgenomes. The existence of the seven <i>Brachypodium</i> progenitor genomes in the polyploids was confirmed by their karyotypic barcode profiles. Comparative phylogenomics of nuclear vs plastid trees allowed us to formulate hypothetical homoploid hybridizations and allo- and autopolyploidization scenarios that could have generated the six <i>Brachypodium</i> polyploids.</p>
FIGURE 2 in A new polyploid species of Limonium (Plumbaginaceae) from the Western Mediterranean basin
FIGURE 2. Limonium irtaensis: (a) spikes; (b) leaves; (c–d) outer bract, adaxial and abaxial surfaces; (e) middle bract; (f) inner bract; (g–h) calyx; (i) fruit. Voucher: A. Navarro, J.A. Rosselló, P. Pérez Rovira & E. Laguna 013001 (Castellón: Peñíscola, Sierra de Irta, 31SBC5695, Castellón, Spain, VAL-226810, holotype). Illustration by Roberto Roselló.
FIGURE 2 in Underestimated diversity in one of the world's best studied mountain ranges: The polyploid complex of Senecio carniolicus (Asteraceae) contains four species in the European Alps
FIGURE 2. Representative shapes of rosette leaves (left) and cauline leaves (right) of Senecio carniolicus (A) and S. noricus (B). Drawings: R. Flatscher.
FIGURE 3 in Underestimated diversity in one of the world's best studied mountain ranges: The polyploid complex of Senecio carniolicus (Asteraceae) contains four species in the European Alps
FIGURE 3. Representative shapes of rosette leaves (left) and cauline leaves (right) of Senecio insubricus (A) and S. disjunctus (B). Drawings: R. Flatscher.
FIGURE 1 in Underestimated diversity in one of the world's best studied mountain ranges: The polyploid complex of Senecio carniolicus (Asteraceae) contains four species in the European Alps
FIGURE 1. Iconography of Senecio carniolicus (A), S. insubricus (B), S. noricus (C) and S. disjunctus (D). Drawings: R. Flatscher.
FIGURE 4 in Underestimated diversity in one of the world's best studied mountain ranges: The polyploid complex of Senecio carniolicus (Asteraceae) contains four species in the European Alps
FIGURE 4. Representative individuals of Senecio carniolicus (A, Almerhorn, population 58 from Sonnleitner et al. 2010), S. insubricus (B; Plose, population 46), S. noricus (C; Bretthöhe, population 80), and S. disjunctus (D; Bretthöhe, population 80). Note the characteristic differences in indumentum density and leaf dissection as well as in the number of capitula per synflorescence. Photographs: M. Sonnleitner.
FIGURE 5 in Underestimated diversity in one of the world's best studied mountain ranges: The polyploid complex of Senecio carniolicus (Asteraceae) contains four species in the European Alps
FIGURE 5. Distribution of the four species of the Senecio carniolicus agg. in the Eastern Alps based on Sonnleitner et al. (2010); S. carniolicus (A), S. insubricus (B), S. noricus (C) and S. disjunctus (D). Morphometrically evaluated populations are marked with a black dot.
FIGURE 1. Mecardonia reneeae. A in A new polyploid species of Mecardonia (Gratioleae, Plantaginaceae) from South America
FIGURE 1. Mecardonia reneeae. A: Habit. B: Stem. C: Detail of the leaf. D: Flower in lateral view. E: Calyx. F: Dissected corolla. G: Anterior anther. H: Posterior anther. I: Gynoecium. J: Fruit (A-C: from Greppi & Hagiwara 560, BAB; illustrated by M. Marino; B–J: from Schinini 11601, CTES; illustrated by Mirtha L. Gómez).
FIGURE 2. A, C in A new polyploid species of Mecardonia (Gratioleae, Plantaginaceae) from South America
FIGURE 2. A, C: Mecardonia procumbens var. flagellaris. A. Habit, C. Metaphase image showing 22 chromosomes. B, D. M. reneeae. B. Habit. D. Metaphase image showing 44 chromosomes.
FIGURE 10 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 10. Pollen of putative aneuploid and nonaploid Caltha, determined by morphology and molecular data (Wefferling & Hoot, unpublished data). ††ploidy level determined by chromosome counts (Wefferling et al. 2015); †ploidy level estimated by flow cytometry (Wefferling et al. 2017). A. Hybrid with morphology of C. biflora, with larger genome size (aneuploid?) than any other sampled C. biflora (Wefferling et al. 2017); U.S.A.: Washington, Hunter, G. LR5† (UWM). B. Non-hybrid with morphology of C. chionophila, with larger genome size (aneuploid?) than any other C. chionophila (Wefferling et al. 2017); U.S.A.: Colorado, Townesmith, A., G. Gust, and L. Nye 202† (UWM). C. Allononaploid (9x) C. leptosepala; U.S.A.: Idaho, Wefferling, K.M. 212rotA†† (UWM).
FIGURE 9 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 9. Pollen of 12x Caltha leptosepala, determined by morphology and molecular data (i.e., two ribotypes were retrieved from each specimen; Wefferling & Hoot, unpublished data). ††ploidy level determined by chromosome counts (Wefferling et al. 2015); †ploidy level estimated by flow cytometry (Wefferling et al. 2017). A. U.S.A.: Washington, Rodman, S., D. Tank, C. Spurgeon, and K. Ardern 909 (WTU). B. Canada: British Columbia, Marr, K., R. Hebda, and W. MacKenzie 06-0013† (RBCM). C. U.S.A.: Alaska, Parker, C.L., A.R. Batten, and D. Blank 9523 (UWM). D. U.S.A.: Alaska, Wefferling, K.M. 63† (UWM). E. U.S.A.: Oregon, Wefferling, K.M. CR5†† (UWM). F. U.S.A.: California, Bartolomew, B. 4327 and B. Anderson (NYBG). G. U.S.A.: Idaho, Parks, M., L. Stratford, and R. McNeill 620† (ID). H. U.S.A.: Oregon, Wefferling, K.M. and L. Woo 62† (UWM). I. Canada: British Columbia, Marr, K., R. Hebda, L. Kennedy, and White 02-48 (RBCM). Size bars = 6 μm.
FIGURE 8 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 8. Pollen of Caltha chionophila, determined by morphology and molecular data (Wefferling & Hoot, unpublished data). †ploidy level estimated by flow cytometry (Wefferling et al. 2017). A. U.S.A.: New Mexico, Holmgren, N.H., and P.K. Holmgren 7330 (NYBG). B. U.S.A.: Colorado, Hall, C., B. Jacobs, and A. Morgan 1565† (NYBG). C. U.S.A.: Nevada, Tiehm, A. and M. Williams 9675 (ID). D. U.S.A.: Utah, Holmgren, N.H., and P.K. Holmgren 15424† (NYBG). E. U.S.A.: Idaho, Errter, B., B. Corbin, C. Scott, J. Irwin, and W. Irwin 20192 (SRP). F. U.S.A.: Wyoming, Wefferling, K.M. 19† (UWM). G. U.S.A.: Oregon, Johanson, J. 07-10 (WTU). H. U.S.A.: Arizona, Rink, G. and L. Stevens s.n. (ASC). I. U.S.A.: Idaho, Wefferling, K.M. 212lepto† (UWM). Size bars = 6 μm.
FIGURE 11 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 11. Close-up photographs of Caltha flowers. A. C. biflora. U.S.A.: Washington, Alpine Lakes Wilderness. Photo by L. Wefferling. B. C. chionophila. U.S.A.: Wyoming, Medicine Bow National Forest. C. C. leptosepala. U.S.A.: Alaska, Chugach National Forest.
FIGURE 6 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 6. Bayesian MCMC phylogram of Caltha species based on nuclear ribosomal DNA (ITS1, 5.8S, and ITS2). Posterior probability (PP) and bootstrap (BS) support is given for each node: PP/MLBS/MPBS.—indicates branch was not found. Dashed branches indicate less than moderate support for at least one approach (PP ≤ 0.95, BS ≤ 70). Dashed lines connect ribotypes from a single allododecaploid individual. Psychrophila group and Caltha leptosepala complex indicated with vertical bars to right. Ploidy level (x = 8) and collection site is given for each ingroup sample. AK = Alaska, CO = Colorado, ID = Idaho, OR = Oregon, WA = Washington (all U.S.A.).
FIGURE 7 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 7. Pollen of Caltha biflora, determined by morphology and molecular data (Wefferling & Hoot, unpublished data). ††ploidy level determined by chromosome counts (Wefferling et al. 2015); †ploidy level estimated by flow cytometry (Wefferling et al. 2017). A. U.S.A.: Alaska, Koval, V.L. 5 (ALA). B. U.S.A.: Nevada, Johnson, J.M. 097 (NYBG). C. U.S.A.: California, Janeway, L.P. 7564 (CSU). D. U.S.A.: California, Wefferling, K.M. and L. Woo 21 (UWM). E. U.S.A.: California, Wefferling, K.M. and L. Woo 30† (UWM). F. U.S.A.: Washington, Wefferling, K.M. 50† (UWM). G. Canada: British Columbia, Calder, J.A., D.B.O. Savile, and R.L. Taylor 21584 (V). H. U.S.A.: Oregon, Wefferling, K.M. 69† (UWM). I. U.S.A.: Washington, Wefferling, K.M. CR1†† (UWM). Size bars = 6 μm.
FIGURE 4 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 4. Isolectotype of Caltha chionophila, collected by C.F. Baker, 1899. "Near Pagosa Peak, 11,000 ft., Colorado" (U.S.A.). Housed at the Greene-Nieuwland Herbarium, Notre Dame, U.S.A. (NDG17369). Inset photo shows broad filaments; magnified 5×.
FIGURE 2 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 2. Holotype of Caltha leptosepala, collected by A. Menzies, 1792. "Northwest Coast of America, Prince William Sound." (coastal Alaska, U.S.A.). Housed at The Natural History Museum, London, England (BM565602). Inset photo shows narrow filaments; magnified 5×.
FIGURE 1 in Species circumscription of the Caltha leptosepala polyploid complex (Ranunculaceae) based on molecular and morphological data
FIGURE 1. Holotype of Caltha biflora, collected by A. Menzies, 1792. "Northwest coast of America, inland behind Banks Island." (between Haida Gwaii and mainland British Columbia, Canada). Housed at The Natural History Museum, London, England (BM565604). Inset photo shows a single narrow, filiform filament; magnified 5×.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.
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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.