Contributors: Hiroki Ando
... The data products derived and presented in the manuscript of "Venusian cloud distribution simulated by a general circulation model" to Journal of Geophysical Research - Planets. *.grd file is grads format file and *.ctl file is control file of grads data. The detail of the data is given by Sugimoto et al. (2014a and 2014b) and Takagi et al. (2018).
Contributors: Ilias Georgakopoulos Soares
... The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. We introduce a novel way to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our new analytical approach reveals new insights into the contribution of DNA repair towards indel mutagenesis in human cells.
Contributors: Juan_Gabriel Rueda-Bayona
... the folder contains input and setup files of the article An Alternative Method to Determine Extreme Hydrodynamic Forces with Data Limitations for Offshore Engineering
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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.
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, Magrieta 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.
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: Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)
Contributors: Tzu-Tong Kao, Michael Windham, Forrest Freund, Kathleen Pryer, Carl Rothfels
... - Alignment files for 7 molecular markers. [7 files] - Maximum parsimony (MP) trees for 4 nuclear markers. [4 files] - Best maximum likelihood (ML) trees for 4 nuclear marker datasets, and a concatenated plastid (Cp) dataset. [5 files] - Maximum likelihood bootstrap (MLBS) trees (50% majority) for 4 nuclear marker datasets, and a concatenated plastid (Cp) dataset. [5 files] - Bayesian trees for 4 nuclear marker datasets, and a concatenated plastid (Cp) dataset. [5 files] - Species trees for the 4 nuclear markers (Nr) or nuclear markers plus a concatenated plastid dataset (Cp + Nr), where each accession was set as one species (pop), or each currently recognized species is one species (sp). [4 files] - Total 30 files