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  • 1
    Publication Date: 2024-03-06
    Description: The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the \ngenus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based \non barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here \nwe obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated \na phylogeny based on rDNA internal transcribed spacer ITS1, 5.8S and ITS2 (ITS), and a phylogenomic analysis of \n3839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that \nthe genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), \nfour recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic \nanalysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus \nand designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, \nP. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, \nwe synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described \nfive new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis.
    Keywords: Agaricaceae ; ecology ; fungaria ; geography ; museomics ; novel species ; phylogenomics ; Podaxis ; typification
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 2
    Publication Date: 2023-11-02
    Description: In this study, we measured the relative transcript expression of 45 target genes and 3 normalizer genes in liver samples of 120 Atlantic salmon that were subjected to 3 different climate scenarios in a tank-based system. Atlantic salmon were exposed to following treatments: (1) Control (CT) constant temperature of 12°C and 100 % air saturation; (2) Warm&Normoxic (WN) incremental temperature increase (1°C per week from 12 - 20°C) at 100% air saturation; and (3) Warm&Hypoxic (WH) decrease in oxygen content of 70% air saturation over one week, followed by two weeks of acclimation to this oxygen level, and then incremental temperature increase (1°C per week from 12 - 20°C) at 70% air saturation. Liver samples were taken from 8 fish per treatment group (CT, WN and WH) at 5 different temperature measuring points: 12°C, 16°C, 18°C, 19°C, and 20°C. For each treatment group, we used 8 biological fish replicates (4 fish from 2 tank replicates). The sampling during the simulated seasonal temperature increase was performed 3 days after reaching the temperature level of interest (12°C-initial, 16°C-3days, 18°C-3days, 19°C-3days, 20°C-3days). Once the maximum temperature increase of 20°C was reached, an additional sampling after 4 weeks at 20°C was carried out (20°C-4weeks). After each temperature challenge eight fish per per tank replicate (n = 8, N = 24) were euthanized with 400 mg L^-1 of tricaine-methane-sulfonate. Liver tissues (100 mg per sample) were rapidly dissected from fish, placed in RNase-free 1.5 mL tubes, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extractions were performed. The relative transcript expression values of 45 genes of interest (GOIs) and 3 normalizers were assessed for 8 individual fish samples per 3 treatment groups at 5 sampling time points (n = 8, N = 120). Real-time qPCR Fluidigm Biomark HD system based on 96.96 dynamic arrays (GE-arrays) was employed according to the manufacturer's instructions (Fluidigm, Biomark HD). The transcript levels of 48 genes were measured in two technical replicates, while we included two no template controls (NTCs), two controls for genomic DNA contamination (no-reverse transcription 'no-RT') and two linker samples for inter-run and between-run calibration. In this data submission file, we provide the 'mean threshold cycle (CT) values' for 45 GOIs and 3 normalizer genes that were calculated from two technical replicates and were measured with GE-fast 96.96 PCR protocol and Fluidigm Biomark HD system. This experiment was performed as part of the project 'Mitigating the Impacts of Climate-Related Challenges on Salmon Aquaculture (MICCSA)' within the years 2017-2020.
    Keywords: Aquaculture; Climate change; hypoxia; Increasing Temperatures; Transcriptomics
    Type: Dataset
    Format: application/zip, 105.5 kBytes
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