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Supplementary material 1 from: Saitoh K, Shindo K, Fujimoto Y, Takahashi K, Shimada T (2016) Mitochondrial genotyping of an endangered bitterling Acheilognathus typus (Cyprinidae). ZooKeys 623: 131-141. https://doi.org/10.3897/zookeys.623.8981
Table S1, Figure S1 : Explanation note: Table S1. Normalized haplotype composition of localities.
A combined transcriptome - miRNAome approach revealed that a kinesin gene is differentially targeted by a novel miRNA in an apomictic genotype of Eragrostis curvula
<p>Weeping lovegrass (<em>Eragrostis curvula</em> [Shrad.] Nees) is a perennial grass typically established in semi-arid regions, with good adaptability to dry conditions and sandy soils. This polymorphic complex includes both sexual and apomictic cytotypes, with different ploidy levels (2x-8x). Diploids are known to be sexual, while most polyploids are facultative apomicts, and full apomicts have also been reported. Plant breeding studies throughout the years have focused on achieving the introgression of apomixis into species of agricultural relevance, but, given the complexity of the trait, a deeper understanding of the molecular basis of regulatory mechanisms of apomixis is still required. Apomixis is thought to be associated with silencing or disruption of the sexual pathway, and studies have shown it is influenced by epigenetic mechanisms. In a previous study, we explored the role of miRNA-mRNA interactions using two contrasting <em>E. curvula</em> phenotypes. Here, the sexual OTA-S, the facultative Don Walter and the obligate apomictic Tanganyika cDNA and sRNA libraries were inquired, searching for miRNA discovery and miRNA expression regulation of genes related to the reproductive mode. This allowed for the characterization of seven miRNAs and the validation of their miRNA-target interactions. Interestingly, a <em>kinesin</em> gene was found to be repressed in the apomictic cultivar Tanganyika, targeted by a novel miRNA that was found to be overexpressed in this genotype, suggestive of an involvement in the reproductive mode expression. Our work provided additional evidence of the contribution of the epigenetic regulation of the apomictic pathway.</p>
Microsatellite genotype data for captive and wild Arabian leopards
<p>Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbour genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (<em>Panthera pardus nimr</em>) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modelling approaches. We estimated a population size of 51 (95% CI: 32–79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population, as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realised load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. The next step in the recovery plan of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimise a strategy for genetic rescue as a tool to recover Arabia's last big cat.</p>
FSJ Genotype FInal All Loci
<p>Microsatellite genotype data of Florida Scrub-Jay at Kennedy Space Center</p>
Figure 2 in Prevalence and new genotypes of Enterocytozoon bieneusi in sheltered dogs and cats in Sichuan province, southwestern China
Figure 2. Phylogenetic relationship of Enterocytozoon bieneusi groups, the relationship between E. bieneusi genotypes obtained in the present study and other known genotypes deposited in GenBank was inferred by a neighbor-joining analysis of ITS sequences based on genetic distance by the Kimura-2-parameter model. The numbers on the branches represent percent bootstrapping values from 1000 replicates, with more than 50% shown in the tree. Each sequence is identified by its accession number, genotype, and host. Genotypes obtained in this study are showed in bold.
Figure 1. PCoA plot for the 22 in Morphological, sensory and biochemical characteristics of summer apple genotypes
Figure 1. PCoA plot for the 22 analyzed summer apple genotypes and cv. Summerred (the genotype number codes on the plot refer to morphological and biochemical data).
Data for "Individual, but not population asymmetries, are modulated by social environment and genotype in Drosophila melanogaster"
<p>Dataset and scripts for the manuscript: "Individual, but not population asymmetries, are modulated by social environment and genotype in <em>Drosophila melanogaster". </em>We upload:</p> <p>1.Data. This directory contains the raw tracking data used for the analysis and the calibration files required by Flytracker for each strain of the Drosophila Genetic Reference Panel (RAL-69, RAL-136, RAL-338, RAL-535, RAL-796).<br> The format of the dataset consists in the output of tracking the (x,y) position and related features (e.g. velocity, distance) of flies in a circular arena using the software Flytracker - http://www.vision.caltech.edu/Tools/FlyTracker/ - For each video we have a trak.mat file and a feat.mat file. For instance, for a video in which we tracked the DGRP line RAL-136 (d338), with a pair of males (mm), trial 3 (t5) we had as outputs d338mmt5joined-feat.mat and d338mmt5joined-track.mat . You can find the description of the output here: http://www.vision.caltech.edu/Tools/FlyTracker/documentation.html</p> <p>2.Load_data _and_circling_scripts. This directory contains a MATLAB file with the instructions on how to load datasets and how to compute the circling index.</p> <p>3.Heatmap. This directory contains the instructions (readme_heatmap.txt) and scripts to (a) fix a bug in the feat files ouput by Flytracker using the calibration files and the script feat_compute_revised.m (b) plot the heatmap of the position and distance between partner flies in a dyad.</p>
Figure 1 in Antibiosis in soybean genotypes to Spodoptera cosmioides (Lepidoptera: Noctuidae)
Figure 1 Dendrogram resulting from the multivariate grouping analyses, using the UPGMA method, based on the Mahalanobis distance, from the LP (Larval period - days), PP (Pupal period - days), LW (Larval weight - mg), PW (Pupal weight - mg), LC (Life cycle - days) and TV (Total viability – percentage) in soybean genotypes for resistance to Spodoptera cosmioides (Lepidoptera: Noctuidae). Urutaí, Goiás, Brazil.
Figure 2 in Antibiosis in soybean genotypes to Spodoptera cosmioides (Lepidoptera: Noctuidae)
Figure 2 Biplot containing average scores of 18 soybean genotypes for resistance to Spodoptera cosmioides (Lepidoptera: Noctuidae).Evaluated characters:LP (Larval period - days), PP (Pupal period - days), LW (Larval weight - mg), PW (Pupal weight - mg), LC (Life cycle - days).
Fig. 1 in Genotypes and zoonotic potential of Enterocytozoon bieneusi in edible bullfrogs (Lithobates catesbeiana) in China
Fig. 1. Nucleotide sequence analysis of the newly identified E. bieneusi genotypes (BLC1 to BLC19) based on the ITS regions, as compared with the known genotype EbpC (AF135832) (synonym with genotype E).
Early Assessment of Drought Tolerance in Cotton Genotypes at seedling stage
<p>Early Assessment of Drought Tolerance in Cotton Genotypes at <br>seedling stage </p>
Characterization of Rapseed (Brassica napus) Genotypes on the basis of Phenotypic Traits
<p>Characterization of Rapseed (Brassica napus) Genotypes on the basis of Phenotypic Traits </p>
Table 2 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
<p><b>Table 2</b> Summary of the annotation of the sweetpotato unigenes.</p><table><tbody><tr><th></th><th>Number of unigenes</th><th>Percentage (%)</th></tr></tbody><tbody><tr><th>Total unigenes</th><td>109,401</td><td></td></tr><tr><th>Annotated in NR</th><td>41,729</td><td>38.14</td></tr><tr><th>Annotated in NT</th><td>21,004</td><td>19.19</td></tr><tr><th>Annotated in KO</th><td>12,524</td><td>11.44</td></tr><tr><th>Annotated in SwissProt</th><td>29,444</td><td>26.91</td></tr><tr><th>Annotated in PFAM</th><td>30,212</td><td>27.61</td></tr><tr><th>Annotated in GO</th><td>31,304</td><td>28.61</td></tr><tr><th>Annotated in KOG</th><td>14,349</td><td>13.11</td></tr><tr><th>All annotated unigenes</th><td>47,749</td><td>43.64</td></tr></tbody></table>
Table 3 in Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis
<p><b>Table 3</b> Summary of EST-SSRs in the sweetpotato transcriptome.</p><table><tbody><tr><th>Searching item</th><th>Numbers</th></tr></tbody><tbody><tr><th>Total number of sequences examined</th><td>109,401</td></tr><tr><th>Total size of examined sequences (bp)</th><td>75,954,853</td></tr><tr><th>Total number of identified SSRs</th><td>9549</td></tr><tr><th>Number of SSR containing sequences</th><td>8334</td></tr><tr><th>Number of sequences containing more than 1 SSR</th><td>1025</td></tr><tr><th>Number of SSRs present in compound formation</th><td>399</td></tr><tr><th>Di-nucleotide</th><td>5086</td></tr><tr><th>Tri-nucleotide</th><td>4092</td></tr><tr><th>Tetra-nucleotide</th><td>336</td></tr><tr><th>Penta-nucleotide</th><td>19</td></tr><tr><th>Hexa-nucleotide</th><td>16</td></tr></tbody></table>
Data from: Mating system of Caiman yacare (Reptilia Alligatoridae) described from microsatellite genotypes
The yacare caiman (Caiman yacare) is a reptile from South America and 1 of the 2 crocodilian species present in Argentina. The degradation of their natural habitat and strong hunting pressure led to a sharp numerical decline of wild populations. Nowadays, C. yacare is included in Appendix II of CITES, and ranching practices in some areas in Argentina are helping hatching success. In this context, it is important to better understand the population structure and mating system of the species. To do this, we amplified 10 microsatellite markers (SSRs) in 148 individuals of 13 C. yacare nests. All of the markers were polymorphic with 2–12 alleles per locus, with allelic sizes ranging between 154 and 400 bp and medium levels of polymorphism (H o = 0.152–0.551 and H e = 0.221–0.621). We were able to determine the maternal genotype in 9 out of 13 nests. In 6 of them we found more than 1 paternal genotype, with a maximum of 3 fathers for a single nest. This study is the first to provide evidence of multiple paternity behavior. These findings will be useful to improve management and conservation strategies for the species.
Data from: Genotypic covariance between the performance of a resident species and community assembly in the field
1.Genetic variation in resident species can influence the assembly and dynamics of communities, but the potential for these genetic effects to persist across generations is largely unresolved. In principle, persistent, directional changes in communities are only predicted when community properties covary genetically with the fitness of resident species. 2.Estimates of genetic covariance between the fitness of a resident species and its community are therefore necessary to 'close the eco-evolutionary loop' in studies of community genetics, but such estimates are rare. Emulating community genetics experiments in plants, we used clonal replicates of 21 genotypes of a resident species (the encrusting bryozoan, Hippopodina) to investigate the magnitude of genotypic variance contributing to assembly of a marine benthic community. 3.Genotypes explained up to 35% of variation in community assembly. Critically, the performance of Hippopodina genotypes covaried both with the evenness of communities, and with the abundances of some individual species, representing an indirect genetic effect that creates the potential for multigenerational interactions between Hippopodina and co-existing species. Our results suggest that different genotypes will associate with different community members consistently across generations, and such non-random associations can give rise to specialization. Further interactions between species other than Hippopodina itself may also be altered by effects of genetic variation in the focal species. 4.Furthermore, species in the community other than Hippopodina itself will interact more commonly in the presence of some genotypes over others. 5.Our results support the potential for genetic variation in one species to have deterministic effects on the dynamics of ecological communities.
Data from: Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping by sequencing data from natural populations
Whole genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: 1) the expected frequency of heterozygotes exceeds that for singleton loci, and 2) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci. These deviations are often not apparent within individuals, particularly when sequence coverage is low; but, we postulated that summing allele reads for each locus over all heterozygous individuals in a population would provide sufficient power to detect deviations at those loci. We identified paralogous loci in three species: Chinook salmon (Oncorhynchus tshawytscha) which retains regions with ongoing residual tetrasomy on eight chromosome arms following a recent whole genome duplication, mountain barberry (Berberis alpina) which has a large proportion of paralogs that arose through an unknown mechanism, and dusky parrotfish (Scarus niger) which has largely re-diploidized following an ancient whole genome duplication. Importantly, this approach only requires the genotype and allele-specific read counts for each individual, information which is readily obtained from most GBS analysis pipelines.
Data from: The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster
Here we present a statistically rigorous approach to quantifying microarray expression data that allows the relative effects of multiple classes of treatment to be compared and incorporates analytical methods that are common to quantitative genetics. From the magnitude of gene effects and contributions of variance components, we find that gene expression in adult flies is affected most strongly by sex, less so by genotype and only weakly by age (for 1- and 6-wk flies); in addition, sex x genotype interactions may be present for as much as 10% of the Drosophila transcriptome. This interpretation is compromised to some extent by statistical issues relating to power and experimental design. Nevertheless, we show that changes in expression as small as 1.2-fold can be highly significant. Genotypic contributions to transcriptional variance may be of a similar magnitude to those relating to some quantitative phenotypes and should be considered when assessing the significance of experimental treatments.
Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes. In this study, we utilized RNA-seq to assess transcriptome-wide gene expression in the muscle of Atlantic killifish (Fundulus heteroclitus) from a population that contains segregating variation in mitochondrial genotype. We examined gene expression plasticity in response to 5°C acclimation and the effects of mitochondrial genotype on this plasticity. Cold acclimation resulted in changes in gene expression consistent with up-regulation of genes involved in many cellular functions, including spliceosomal and proteasomal processes, and with down-regulation of genes involved in extracellular matrix, muscle contraction and oxidative phosphorylation functions. There were few differences in gene expression between killifish with different mitochondrial genotypes: 14 genes demonstrated significant interactions between mitochondrial genotype and acclimation temperature and 3 genes demonstrated effects of mitochondrial genotype alone. These results indicate that variation in mitochondrial genotype has modest effects on gene expression; the majority of which are revealed as differences in plasticity as a result of environmental change.
Data from: High-throughput genotyping of green algal mutants reveals random distribution of mutagenic insertion sites and endonucleolytic cleavage of transforming DNA
A high-throughput genetic screening platform in a single-celled photosynthetic eukaryote would be a transformative addition to the plant biology toolbox. Here, we present ChlaMmeSeq (Chlamydomonas MmeI-based insertion site Sequencing), a tool for simultaneous mapping of tens of thousands of mutagenic insertion sites in the eukaryotic unicellular green alga Chlamydomonas reinhardtii. We first validated ChlaMmeSeq by in-depth characterization of individual insertion sites. We then applied ChlaMmeSeq to a mutant pool and mapped 11,478 insertions, covering 39% of annotated protein coding genes. We observe that insertions are distributed in a manner largely indistinguishable from random, indicating that mutants in nearly all genes can be obtained efficiently. The data reveal that sequence-specific endonucleolytic activities cleave the transforming DNA and allow us to propose a simple model to explain the origin of the poorly understood exogenous sequences that sometimes surround insertion sites. ChlaMmeSeq is quantitatively reproducible, enabling its use for pooled enrichment screens and for the generation of indexed mutant libraries. Additionally, ChlaMmeSeq allows genotyping of hits from Chlamydomonas screens on an unprecedented scale, opening the door to comprehensive identification of genes with roles in photosynthesis, algal lipid metabolism, the algal carbon-concentrating mechanism, phototaxis, the biogenesis and function of cilia, and other processes for which C. reinhardtii is a leading model system.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.