Data for: Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data
Contributors: xiuguang mao, Georgia Tsagkogeorga, Stephen Rossiter, Vu Dinh Thong
... cytb_sanger_sinicus12.fas : Twelve cytb sequences generated by Sanger sequencing.
Contributors: Jeny Bastida, Alejandro Crampet, Melitta Meneghel, Victor Morais
... This dataset correspond to the proteomic analysis of the article entitle “Preliminary Biochemical and Venomic Characterization of the Venom of Phalotris lemniscatus (Serpentes, Colubridae)” sending to Current topics in medicinal chemistry. The data set include the raw files of each band of mass spectroscopy and the database used to identify the proteins. To observe the SDS page, please refer to the article. “Protein bands were excised and sent to the Spectroscopy and Biophysics Core, University of Nebraska, Lincoln (via Science Exchange) to in-gel trypsin digestion and peptide fragmentation by LC-MS/MS. The instrument was an LTQ Velos Pro (Thermo Scientific) equipped with dual pressure ion-trap. Raw data obtained by proteomic analysis was analyzed using MaxQuant software [30–32] with the default parameters (false discovery rate 0,01). As a sequence database to match for protein identification, a fasta file download from Uniprot was used. Database was constituted by all the reviewed sequenced proteins of snakes, around 2500 proteins from Swiss-Prot database (taxonomy:"Serpentes (snakes) " AND reviewed:yes)”.
An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae).
Contributors: Daniel Huston
... The following data relates to the manuscript "An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae)." which was accepted by the International Journal for Parasitology on 3 July 2019.
Contributors: Peter Seeber, Gayle McEwen, Ulrike Löber, Daniel Förster, Marion East, Jörg Melzheimer, Alex Greenwood
... 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 for: Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: a case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)
Contributors: Keping Sun, Vu Dinh Thong, Kangkang Zhang, Jiang Feng, Hanbo Zhao, Lin Zhang, Tong Liu, YANYAN XIAO, Longru Jin, Gábor Csorba
... Raw data sets, including mitochondrial sequences, nuclear sequences, microsatellite data and GBS data used in this study.
Data for: Genomic regions associated with mycelial growth and host specificity in Ceratocystis pathogens
Contributors: Irene Barnes, Brenda Wingfield, Magriet van der Nest, Michael Wingfield, Arista Fourie, Lieschen de Vos
... 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.
nad2 (714bp) and nad5 (680bp) alignment of 93 Echinococcus granulosus sensu lato genotype G6 and G7 (including G7a and G7b) sequences
Contributors: Teivi Laurimäe, Liina Kinkar, Urmas Saarma
... 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.
Contributors: Arista Fourie
... 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.
Contributors: Storm Martin
... 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 for: Activity characterization of the plantain promoter from the heavy metal-associated isoprenylated plant gene (MabHIPP) using the luciferase reporter gene
Contributors: Efren Santos
... Promoter sequence of the plantain 'THP' HIPP gene