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  • Mitogenome sequence alignments from DNA isolated from water and sediment samples following hybridization capture enrichment. Abstract: Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystems where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for non-invasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment, and water filtered through glass fiber filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera produced fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of non-target mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.
    Data Types:
    • Sequencing Data
    • Dataset
  • Raw data sets, including mitochondrial sequences, nuclear sequences, microsatellite data and GBS data used in this study.
    Data Types:
    • Other
    • Software/Code
    • Sequencing Data
    • Dataset
  • This data provides the MinION genome sequence data for the two genomes used in linkage map and QTL analyses of Ceratocystis fimbriata and C. manginecans. The genomes consist of long sequence reads, obtained from MinION sequence data, to provide improved contig assemblies, and Illumina sequence data to improve base call quality. The dataset also provides a python script that was used to convert the VCF file obtained from GATK to a binary code of A and B; the format required for JoinMap software for linkage map construction.
    Data Types:
    • Software/Code
    • Sequencing Data
    • Dataset
  • Fasta file with alignment of concatenated nad2 (714 bp) and nad5 (680 bp) sequences of E. granulosus s.l. genotype clusters G6 and G7 (including haplogroups G7a and G7b) for G6-G7 genotype and haplogroup G7a-G7b identification.
    Data Types:
    • Sequencing Data
    • Dataset
  • This data provides the MinION assembled genomes that were used in the article "QTL mapping of mycelial growth and aggressiveness to distinct hosts in Ceratocystis pathogens" by Fourie et al. 2019. These genomes contain MinION sequence reads as well as Illumina HiSeq sequence reads. The data also contains a python script that was used to convert the SNP data to binary data used for downstream analyses.
    Data Types:
    • Software/Code
    • Sequencing Data
    • Dataset
  • Trimmed and untrimmed 28S + 18S rRNA genes alignment for the Opecoelidae (Trematoda) used as evidence for the proposal of a new subfamily, the Pseudoplagioporinae, see: Martin SB, Cutmore SC & Cribb TH (2019). The Pseudoplagioporinae, a new subfamily in the Opecoelidae Ozaki, 1925 (Trematoda) for a small clade parasitising mainly lethrinid fishes, with three new species. Journal of Systematic Zoology and Evolutionary Research
    Data Types:
    • Software/Code
    • Sequencing Data
    • Dataset
  • Promoter sequence of the plantain 'THP' HIPP gene
    Data Types:
    • Sequencing Data
    • Dataset
  • The use of biostimulants induce the expression of genes involved in different metabolic pathways, and may be involved in plant response after pathogen infection. A bioassay was designed using banana plants, derived from in vitro propagation. Plants were grown in pots at greenhouse conditions, and inoculated with the pathogen Pseudocercospora fijiensis (2*10^4 conidia/ml), treatments included the application of a biostimulant (30%) and mock (H2O) application. The biostimulant is a liquid solution that was elaborated in greenhouse using anaerobic microorganisms with plant and organics remains. This solution was used as a biostimulant. To identify differentially expressed genes, associated to the plant response and detection of the pathogen, we used the subtractive suppressive hybridization (SSH) strategy. Two separated libraries were generated, (i) biostimulant application directly to the leaves of banana plants (L1), and (ii) application of biostimulant directly to the soil (L2). A total of 176 unique SSH sequences for the library of foliar application (L1) and 116 unique SSH sequences for the soil application (L2) were isolated, and were analyzed using the Blast2Go software. Highlighted results for L1 and L2 genes identified were related to metabolic process (biological process) and binding (molecular function).
    Data Types:
    • Sequencing Data
    • Dataset
  • Genotyping data of common genetic variations associated with the persistence of immunity following childhood immunisation
    Data Types:
    • Other
    • Geospatial Data
    • Sequencing Data
    • Dataset
    • Text
  • P311 protein structure PDB file
    Data Types:
    • Sequencing Data
    • Dataset
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