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537 results for “Structural Genomics”
Data from: Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera
<p>Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.</p>
Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene-flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability", highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9% of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after 10 replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1102 SVs carried by 52.4 to 80.1% of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
Common barriers, but temporal dissonance: genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community
<p>Assessments of spatial and temporal congruency across taxa from genetic data provide insights into the extent to which similar processes structure communities. However, for coastal regions that are affected continuously by cyclical sea-level changes over the Pleistocene, congruent interspecific response will not only depend upon co-distributions, but also on similar dispersal histories among taxa. Here, we use SNPs to test for concordant genetic structure among four co-distributed taxa of freshwater fishes (Teleostei: Characidae) along the Brazilian Atlantic coastal drainages. Based on population relationships and hierarchical genetic structure analyses, we identify all taxa share the same geographic structure suggesting the fish utilized common passages in the past to move between river basins. In contrast to this strong spatial concordance, model-based estimates of divergence times indicate that despite common routes for dispersal, these passages were traversed by each of the taxa at different times resulting in varying degrees of genetic differentiation across barriers with most divergences dating to the Upper Pleistocene, even when accounting for divergence with gene flow. Interestingly, when this temporal dissonance is viewed through the lens of the species-specific ecologies, it suggests that an ecological sieve influenced whether species dispersed readily, with an ecological generalist showing the highest propensity for historical dispersal among the isolated rivers of the Brazilian coast (i.e., the most recent divergence times and frequent gene flow estimated for barriers). We discuss how our findings, and in particular what the temporal dissonance, despite common geographic passages, suggest about past dispersal structuring coastal communities as a function of ecological and paleo-landscape sieves.</p>
FISH datasets used in Zou et al. integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
<p>This upload contains the FISH datasets used in Zou et al. integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.</p> <p>If you use the datasets, we would be grateful if you cited the following paper:</p> <p>Zou, C., Zhang, Y., Ouyang, Z. (2016) HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure. Genome Biology, 17: 40.</p>
Of Mojave milkweed and mirrors: The population genomic structure of a species impacted by solar energy development
<p>A rapid renewable energy transition has facilitated the development of large, ground‐mounted solar energy facilities worldwide. Deserts, and other sensitive aridland ecosystems, are the second most common land‐cover type for solar energy development globally. Thus, it is necessary to understand existing diversity within environmentally sensitive desert plant populations to understand spatiotemporal effects of solar energy siting and design. Overall, few population genomic studies of desert plants exist, and much of their biology is unknown. To help fill this knowledge gap, we sampled Mojave milkweed (<em>Asclepias</em> <em>nyctaginifolia</em>) in and around the Ivanpah Solar Electric Generating Station (ISEGS) in the Mojave Desert of California to understand the species' population structure, standing genetic variation, and how that intersects with solar development. We performed Restriction‐site Associated Sequencing (RADseq) and discovered 9942 single nucleotide polymorphisms (SNPs). Using these data, we found clear population structure over small spatial scales, suggesting each site sampled comprised a genetically distinct population of Mojave milkweed. While mowing, in lieu of blading, the vegetation across the solar energy facility's footprint prevented the immediate loss of the ISEGS Mojave milkweed population, we show that the effects of land‐cover change, especially those impacting desert washes, may impact long‐term genetic diversity and persistence. Potential implications of this include a risk of overall loss of genetic diversity, or even hastened extirpation. These findings highlight the need to consider the genetic diversity of impacted species when predicting the impact and necessary conservation measures of large‐scale land‐cover changes on species with small population sizes.</p>
A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
<p>Quinoa (<em>Chenopodium</em> <em>quinoa</em> Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for three accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we used in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned 1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds. The genome was annotated with 54,499 protein-coding genes, 97% of which were located on the 18 largest scaffolds. We also produced an updated genome assembly for the B-genome diploid <em>C. suecicum</em> and used it, together with the A-genome diploid<em> C. pallidicaule</em>, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.20%, 48.61%, and 57.91% of the quinoa, <em>C. pallidicaule</em>, and <em>C. suecicum</em> genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.</p>
Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees
<p>The <em>Asian honeybee</em>, <em>Apis cerana</em>, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of<em> A. cerana</em>. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of <em>A. cerana</em>, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel <em>A. cerana</em> ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of <em>A. cerana</em> by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of <em>A. cerana</em>.</p>
Data from: Two male-killing Wolbachia from Drosophila birauraia that are closely related but distinct in genome structure
<p><a>Insects </a>harbour diverse maternally inherited bacteria and viruses, some of which have evolved to kill the male progeny of their hosts (male killing: MK). The fly species <em>Drosophila biauraria</em> carries a maternally transmitted MK-inducing partiti-like virus, but it was unknown if it carries other MK-inducing endosymbionts. Here, we identified two male-killing <em>Wolbachia</em> strains (<em>w</em>Biau1 and <em>w</em>Biau2) from <em>D. biauraria</em> and compared their genomes to elucidate their evolutionary processes. The two strains were genetically closely related but had exceptionally different genome structures with considerable rearrangements compared with combinations of other <em>Wolbachia</em> strains. Despite substantial changes in the genome structure, the two <em>Wolbachia</em> strains did not experience gene losses that would disrupt the male-killing expression or persistence in the host population. The two <em>Wolbachia</em>-infected matrilines carried distinct mitochondrial haplotypes, suggesting that <em>w</em>Biau1 and <em>w</em>Biau2 have invaded <em>D. biauraria</em> independently and undergone considerable genome changes owing to unknown selective pressures in evolutionary history. This study demonstrated the presence of three male-killers from two distinct origins in one fly species and highlighted the diverse and rapid genome evolution of MK <em>Wolbachia </em>in the host.</p>
Data from: Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean
<p><strong>Aim</strong> Efficiently protecting species requires knowing their ecological, life history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus <em>Pocillopora</em> found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity.</p> <p><strong>Location</strong> Archipelagos and islands of the southwestern Indian Ocean.</p> <p><strong>Taxon</strong> <em>Pocillopora </em>spp.</p> <p><strong>Methods</strong> We used target-capture to collect single-nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1,400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population.</p> <p><strong>Results</strong> All four <em>Pocillopora</em> species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger ( <em>F<sub>ST</sub></em> about 10 times higher) for <em>P. acuta</em>, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from <em>P. acuta</em>, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period.</p> <p><strong>Main conclusions</strong> These results indicate reduced gene flow between Madagascar and the Mascarenes, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change.</p>
Data from: Genomic diversity and structure of a Neotropical microendemic fig tree
<p>Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is <em>Ficus (Moraceae)</em>. It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of <em>Ficus</em> species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of <em>Ficus</em> <em>pringlei</em> to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. <em>Ficus</em> <em>pringlei</em> populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (F<sub>ST</sub>= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as <em>F</em>. <em>pringlei</em>.</p>
A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants
<h2># Genomic datasets associated to the publication: </h2> <h3># Gene-ID conversion with previous genome version</h3> <p>Texasv3_vs_Texasv2_GeneID.txt -- gene ID conversion between Texasv3 and Texasv2 (https://www.rosaceae.org/analysis/295)</p> <p>pdulcis26_to_F1_liftoff_polished.gff3 -- Texasv2 gene annotation liftoff on Phase-1 assembly (Phase-1 coordinates)</p> <h3># Phase-1</h3> <p>Texas_F1_K80_chr.fasta -- genome asssembly, phase-1 <br>Texas_F1_gene_models.gff3 -- phase-1 gene annotation (de novo annotation)<br>Functional_annotation_TexasF1.csv -- phase-1 gene functions <br>Texas_F1_ref_SV.vcf --- Structural variations relative to phase-0 (This file uses Phase-1 as reference)</p> <h3># Phase-0</h3> <p>Texas_F0_K80_chr.fasta -- genome asssembly, phase-0 <br>Texas_F0_gene_models.gff3 -- phase-0 gene annotation (liftoff from Phase-1)<br>Functional_annotation_TexasF0.csv -- phase-0 gene functions <br>Texas_F0_ref_SV.vcf --- Structural variations relative to phase-1 (This file uses Phase-0 as reference)</p> <h3># Transposable element annotation</h3> <p>Texas_F0_HiConf_TE_v3.gff3 --- TE annotation in Phase-0<br>Texas_F1_HiConf_TE_v3.gff3 --- TE annotation in Phase-1<br>Texasv3_TElib.fa --- TE library of TexasV3 (non-redundant repeat consensuses taking the account the two genome phases)</p> <h3># Gene sequences in fasta</h3> <p>Transcript, CDS and protein sequences in fasta format for phase-0 (F0) and phase-1 (F1) </p>
Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome
<p>Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.</p>
Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection
<p>Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic relationships from pedigree data [(n=64,310 animals recorded in the U.S. National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n=18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (N<sub>e</sub>) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (H<sub>E</sub>) and observed (H<sub>O</sub>) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the U.S. population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by F<sub>ST</sub>. Using these measures of genetic diversity, a framework for establishing a genomic reference population in U.S. Suffolk sheep engaged in NSIP was proposed.</p>
Data from: Population genomics reveal deep divergence and strong geographical structuring in the Hengduan Mountains
<p>We used restriction site-associated DNA sequencing to generate 1,907 single nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the <em>Gentiana hexaphylla</em> complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing the diversification of <em>G</em>. <em>hexaphylla</em> in the HM. Here, the SNP data and plastid sequence alignments are provided.</p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
<p><strong>Summary</strong></p> <p>Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for <em>H<sub>O</sub></em> and <em>H<sub>E</sub></em> was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.</p>
Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru
<p>Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production regions in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (H<sub>e</sub>), observed heterozygosity (H<sub>o</sub>), and inbreeding coefficient (F<sub>IS</sub>) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with H<sub>o</sub> values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p< 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.</p>
Bryozoan genomes reveal extensive chromosome rearrangement and the evolution of bilaterian genome structure
<p>Orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, can be seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the importance of genome organization to gene regulatory landscapes. Here, we report a unique pattern of genome evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, including phylogenetic reconstruction and orthologous gene mapping, we reconstruct the chromosomal evolutionary history of five bryozoans. We infer the ancestral bryozoan genome organization and identify multiple ancient chromosome fusions followed by gene mixing, leading to the near-complete loss of bilaterian linkage groups. A second wave of rearrangements, including chromosome fission, occurred independently in two bryozoan classes, further shuffling bryozoan genomes. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional yet highly debated Lophophorata hypothesis. Finally, we show that chromosome fusion and fission processes led to the separation of bryozoan Hox clusters. Our findings demonstrate that the canonical bilaterian genome structure has been lost across an entire phylum, reveal that linkage group fission can occur very frequently in specific lineages, and provide a powerful source of phylogenetic information.</p>
Data from: Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish
<p><span>The responses of marine species to environmental changes and anthropogenic pressures (e.g. fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources.</span><span> Almaco jack (<em>Seriola rivoliana</em>) is<em> </em>a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. </span><span>In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Utilizing a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of cl</span><span>imate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100.</span><span> Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. Contemporary genomic structure showed three populations—two in the Eastern Pacific (</span><span>Cabo San Lucas </span><span>and Eastern Pacific) and one in the Central Pacific (</span><span>Hawaii</span><span>). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of <em>S. rivoliana</em> and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects in fisheries that depend on this resource.</span></p>
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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.