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Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

Water yam (Dioscorea alata L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about Dioscorea species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 D. alata accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.17 to 0.74, with a mean of 0.49, which suggests moderate genetic diversity of D. alata accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 91% of the variation was attributed to within-population while among-population contributed 9% of the total variation. The highest Nei's genetic distance (0.65) was for accessions sampled from Arusha and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped D. alata accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of D. alata accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of D. alata accessions for breeding programs in Tanzania.

Data for: From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator

The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3,400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviours, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.

Data for: A selfish genetic element and its suppressor causes abnormalities to testes in a fly

Selfish genetic elements (SGEs), specifically X-chromosome meiotic drive (XCMD), create huge conflicts within a host's genome and can have profound effects on fertility. Suppressors are a common evolutionary response to XCMD to negate its costs. However, whether suppressors themselves can cause negative non-target effects remains understudied. Here, we examine whether the intragenomic conflicts created by XCMD and its suppressor affect gonad morphology in Drosophila subobscura. We found significant differences in testes, seminal vesicle, and accessory gland size depending on whether a male carried a non-driving X chromosome, an XCMD, and if the XCMD was suppressed. We also found the first evidence of abnormal testes development that is specifically associated with a suppressor of XCMD. Unlike other studies, our evidence suggests that XCMD in D. subobscura creates major abnormalities to male gonads. These abnormalities are most frequent if both XCMD and its suppressor are both present. While costs of suppression have importance in theoretical models, they have largely been ignored in empirical XCMD systems. Overall, this study highlights that genetic conflict, created by SGEs and their suppressors, is a potent evolutionary force that can have major impacts on gonad development and gametogenesis.

Steady-state and time-resolved data for the article "Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222"

1. Steady-state data Spectra were taken with/without continuous irradiation with a wavelength of 450 nm. 1.1 CNF absorption region (2200-2260 cm-1) 1.2. Amide absorption region (1500-1800 cm-1) 1.3. UV/Visible absorption region (320-550 nm) Each spectral region has 3 datasets: - DARK - LIT (photostationary state) - DIFFERENCE (lit-minus-dark) The first row contains the variants. The first column contains the wavenumber (in cm-1) or wavelength (in nm). 2. Time-resolved data. Dark recovery reaction after switching lights off (wavelength of 450 nm). 2.1. EL222_WT_H2O 2.2. EL222_WT_D2O 2.3. EL222_W31CNF 2.4. EL222_L35CNF 2.5. EL222_N53CNF 2.6. EL222_Y136CNF 2.7. EL222_M151CNF 2.8. EL222_L216CNF 2.9. EL222_LOV_H2O 2.10. EL222_LOV_D2O For each variant we have measured 3 spectral regions (except for 2.1, 2.2., 2.9 and 2.10, which lack CNF): - CNF: 2200-2270 cm-1 - AMIDE: 1500-1750 cm-1 - UVVIS: 320-550 nm For each probe we have 2 datasets: - DATA: the experimental lit-minus-dark absorbance difference spectra.  The first row contains the time delays (in seconds). The first column contains the wavenumbers (in cm-1) or wavelength (in nm). - LDA: the lifetime density maps calculated from the corresponding DATA using the inverse Laplace transform and maximum entropy penalty. The first row contains the lifetimes (in seconds). The first column contains the wavenumbers (in cm-1) or wavelength (in nm). If you use these datasets please cite: Chaudhari, A.S.; Chatterjee, A.; Domingos, C.A.O.: Andrikopoulos, P. C.; Liu, Y.; Andersson, I.; Schneider, B.; Lórenz-Fonfría, V.A.; Fuertes, G. Genetically Encoded Non-canonical Amino Acids Reveal Asynchronous Dark Reversion of Chromophore, Backbone and Side-chains in EL222. Protein Science. 2023 <a href="https://doi.org/10.1002/pro.4590">https://doi.org/10.1002/pro.4590</a>

Additional Files for "Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass"

This dataset contains additional supporting files referenced by the following publication: • Kersten S, Chang J, Huber CD, Voichek Y, Lanz C, Hagmaier T, Lang P, Lutz U, Hirschberg I, Lerchl J, Porri A, Van de Peer Y, Schmid K, Weigel D, Rabanal FA. Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass. Proc Natl Acad Sci USA.   Directory structure: <ul> <li>Haplotypes_ACCase: this directory contains the two haplotypes (fasta format) inferred by pbaa (https://github.com/PacificBiosciences/pbAA ) for each of the 1,046 individuals for which it was possible to analyse the ACCase locus. </li> </ul>   <ul> <li>Haplotypes_ALS: his directory contains the two haplotypes (fasta format) inferred by pbaa (https://github.com/PacificBiosciences/pbAA ) for each of the 842 individuals for which it was possible to analyse the ALS1 locus. </li> </ul>   <ul> <li>Reference_genome: this directory contains the Pacbio CLR+Hi-C based chromosome level assembly (fasta file) of an Alopecurus myosuroides individual from the German herbicide-sensitive population DE01087 (Appels Wilde Samen GmbH, Darmstadt). In addition, it includes annotation files (gff format) for transposable elements and protein-coding genes.</li> </ul>   <ul> <li>SNP_matrix: this directory contains the SNP matrix (vcf format) for the population study carried out with ddRAD-sequencing data.</li> </ul>

Data for: Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs

Hundreds of genetic variants implicated in Mendelian disease have been characterized in dogs and commercial screening is being offered for most of them worldwide. There is typically limited information available regarding the broader population frequency of variants and uncertainty regarding their functional and clinical impact in ancestry backgrounds beyond the discovery breed. Genetic panel screening of disease variants, commercially offered directly to the consumer or via a veterinary clinician, provides an opportunity to establish large-scale cohorts with phenotype data available to address open questions related to variant prevalence and relevance. We screened the largest canine cohort examined in a single study to date (1,054,293 representative dogs from our existing cohort of 3.5 million; a total of 811,628 mixed breed dogs and 242,665 purebreds from more than 150 countries) to examine the prevalence and distribution of a total of 250 genetic disease-associated variants in the general population. Electronic medical records from veterinary clinics were available for 43.5% of the genotyped dogs, enabling the clinical impact of variants to be investigated. We provide detailed frequencies for all tested variants across breeds and find that 57% of dogs carry at least one copy of a studied Mendelian disease-associated variant. Focusing on a subset of variants, we provide evidence of full penetrance for 10 variants, and at minimum plausible evidence for clinical significance of 22 variants, on diverse breed backgrounds. Specifically, we report that inherited hypocatalasia is a notable oral health condition, confirm that factor VII deficiency presents as subclinical bleeding propensity and verify two genetic causes of reduced leg length. We further assess genome-wide heterozygosity levels in over 100 breeds and show that a reduction in genome-wide heterozygosity is associated with an increased Mendelian disease load. The accumulated knowledge represents a resource to guide discussions on genetic test relevance by breed.

Genetic differentiation of a critically endangered population of the limpet Patella candei candei d'Orbigny, 1840, in the Canary Islands

The adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, P. candei candei d'Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecific relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, P. candei candei was genetically differentiated from the closely related P. candei crenata for the first time. Moreover, genetic differentiation was detected between P. candei candei samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specific management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.

Data from: Evidence of low within-pair genetic relatedness in a relict population of Thorn-tailed Rayadito despite long-term isolation

Investigating whether mating patterns are biased in relation to kinship in isolated populations can provide a better understanding of the occurrence of inbreeding avoidance mechanisms in wild populations. Here we report on the genetic relatedness (r) among breeding pairs in a relict population of Thorn-tailed Rayadito (Aphrastura spinicauda) in north-central Chile that has experienced a long-term history of isolation. We used simulations based on eight years of data to assess whether mating is random with respect to relatedness. We found that mean and median population values of pair relatedness tended to be lower than randomly generated values, suggesting that mating is not random with respect to kinship. We hypothesize that female-biased dispersal is the main mechanism reducing the likelihood of mating among kin, and that the proportion of related pairs (i.e., r > 0.125) in the study population (25%) would presumably be higher in the absence of sex-biased dispersal. The occurrence of other mechanisms such as extra-pair copulations, delayed breeding and active inbreeding avoidance through kin discrimination cannot be dismissed and require further study.

Apatite trace element data for genetic type classification

Apatite trace element data for genetic type classification, including porphyry, skarn, orogenic Au, iron-oxide copper gold (IOCG), and iron-oxide apatite (IOA or Kiruna type).

Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity

1- workflow for data analysis and figures generation

Supplementary Tables for Paper "Hidden genetic regulation of human complex traits via brain isoforms"

Supplementary Tables for Paper "Hidden genetic regulation of human complex traits via brain isoforms".

opencc-by-4.0Dec 2021View details →

Estimating red fox density using non-invasive genetic sampling and spatial capture–recapture modelling

Data and scripts for our paper: Lindsø, L.K., Dupont, P., Rød-Eriksen, L. et al. Estimating red fox density using non-invasive genetic sampling and spatial capture–recapture modelling. Oecologia 198, 139–151 (2022). https://doi.org/10.1007/s00442-021-05087-3

opennotspecifiedMar 2023View details →

FIGURE 1 in Genetic data confirms the enigmatic demosponge Janulum as haplosclerid

FIGURE 1. Maximum likelihood phylogram to highlight the phylogenetic position of Janulum. Newly sequenced taxa are in bold. Numbers following the species names are collection numbers (for the new sequences) or NCBI-Genbank accession numbers. The inset in grey is based on the separate, haplosclerid-only alignment of the same taxa (rooted with Gelliodes callista KC869562 and Xestospongia deweerdtae KP081747). Numbers above branches are RAxML rapid bootstrapping support values (if larger than 70). Scale bars indicate substitutions per site.

opencc-zeroMar 2023View details →

Repository for: Genetic footprints of a rapid and large-scale range expansion: The case of cyclic common vole in Spain

Te repository contains the neccesary genetic data (microsatellite allele frequencies and GenBank accesion numbers for cytb haplotypes) to be able to replicate the analyses performed in the manuscript.

opennotspecifiedMar 2023View details →

FIGURE 3. Correlation between the genetic p in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)

FIGURE 3. Correlation between the genetic p-distances of the barcoding region (cox1) and the 13PCGs of the E. nordenskioldi s.l. taxa.

opencc-by-4.0Mar 2023View details →

Supplementary Table S1 and Supplementary Table S2 - Part of "Next generation leishmanization: revisiting molecular targets for selecting genetically engineered live-attenuated Leishmania"

Supplementary Table S1 and Supplementary Table S2 - Part of "Next generation leishmanization: revisiting molecular targets for selecting genetically engineered live-attenuated Leishmania"

opencc-by-4.0Mar 2023View details →

Data to run analyses present in the paper: Cell specificity of human regulatory annotations and their genetic effects on gene expression

Data for the manuscript: Varshney A., H. VanRenterghem, P. Orchard, A. P. Boyle, M. L. Stitzel, et al., 2019 Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics 211: 549–562. <a href="https://doi.org/10.1534/genetics.118.301525">https://doi.org/10.1534/genetics.118.301525</a> The code to generate these data are at GitHub:  https://github.com/ParkerLab/regulatoryAnnotations_comparisons Also see processed data available in this previous Zenodo record: https://zenodo.org/record/1413623

opencc-zeroDec 2022View details →

The genetic basis of wing spots in Pieris canidia butterflies

Spots in pierid butterflies and eyespots in nymphalid butterflies are likely non-homologous wing colour pattern elements, yet they share a few features in common. Both develop black scales that depend on the function of the gene spalt, and both might have central signalling cells. This suggests that both pattern elements may be sharing common genetic circuitry. Hundreds of genes have already been associated with the development of nymphalid butterfly eyespot patterns, but the genetic basis of the simpler spot patterns on the wings of pierid butterflies has not been investigated. To facilitate studies of pierid wing patterns, we report a high-quality draft genome assembly for Pieris canidia, the Indian cabbage white. We then conducted transcriptomic analyses of pupal wing tissues sampled from the spot and non-spot regions of P. canidia at 3-6h post-pupation. A total of 1,352 genes were differentially regulated between wing tissues with and without the black spot, including spalt, Krüppel-like factor 10, genes from the Toll, Notch, TGF-β, and FGFR signalling pathways, and several genes involved in the melanin biosynthetic pathway. We identified 21 genes that are up-regulated in both pierid spots and nymphalid eyespots and propose that spots and eyespots share regulatory modules despite their likely independent origins.

opencc-by-4.0Apr 2023View details →

Virgin Birth: A genetic basis for facultative parthenogenesis in Drosophila - genome assemblies

Drosophila mercatorum genome assemblies used in https://doi.org/10.1101/2022.03.13.484157. The wildtype assembly is non-parthenogenic, while the "partho" assembly is parthenogenic. Assembly process is described here: https://github.com/ekg/drosophila.