Extensive folding variability between homologous chromosomes in mammalian cells.

Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.

A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.

Midbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage 1-3 . As the synaptic and transcriptional changes that follow an acute cocaine exposure are mostly resolved within a few days 4,5 , the molecular changes that encode the long-term cellular memory of the exposure within DNs remain unknown. To investigate whether a single cocaine exposure induces long-term changes in the 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in the mouse midbrain. We found extensive rewiring of 3D genome architecture at 24 hours past exposure which remains or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. A single cocaine exposure triggers extensive long-lasting changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding of Rbfox1 which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a specific DN sub-type characterized by low expression of the dopamine auto-receptor Drd2 , a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.

SRRM2 splicing factor modulates cell fate in early development.

Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.

Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level.

DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.

Epigenetic regulatory layers in the 3D nucleus.

Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.

Temporal and spatial variability in the isotopic composition of sea urchins along Portuguese coast.

Paracentrotus lividus is a sea urchin widely distributed throughout Mediterranean basin and Atlantic coast, highly appreciated for its gonads. It is broadly distributed along the Portuguese coast and its exploitation has potential to grow. Nevertheless, fluctuations on nutritional composition and sensory traits of P. lividus according to each habitat and seasonality are still little understood. Stable isotopes analysis has been recognised as a powerful tool for exploring environmental-ecological-biological processes in aquatic systems. It is also useful to give indications on how to improve available diets for the aquaculture of this species, contributing to a sustainable rearing. Herein, such technique was used to assess temporal and spatial differences in isotopic composition of P. lividus' gonads and intestines and to evaluate its application as a management tool for the identification of the most suitable locations and periods of the year to collect organisms with high quality gonads. Sampling campaigns were carried out between 2019 and 2020 in five rocky shores along the Portuguese coast (Viana do Castelo, Figueira da Foz, Peniche, Sines and Guia). Three rock pools were selected in each shore, and five specimens were collected per pool. The gonadosomatic index (GSI, %) was calculated and carbon and nitrogen elemental and isotopic composition were determined in gonads and intestine using isotope ratio mass spectrometry. Significant spatial and temporal fluctuations were registered among urchins collected along Portuguese coast. Such variations may be associated with latitudinal gradients along the coast and variations of environmental and ecological conditions within each area, especially those affecting algal biomass, on which urchins primarily feed. More research must be pursued to maximise the use of stable isotopes analysis as a management tool for supporting sustainable exploitation of natural stocks or even to contribute to nutritional studies with new diets for sea urchin production that consider the feeding of these animals in the wild.

Use of the gonadal tissue of the sea urchin Paracentrotus lividus as a target for environmental contamination by trace metals.

Many environmental monitoring works have been carried out using biomarkers as a tool to identify the effects of oil contamination on marine organisms; however, only a few studies have used sea urchin gonadal tissue for this purpose. Within this context, the present work aimed to understand the impact of an oil spill, proposing the use of sea urchin gonadal tissue as a biomarker for environmental contamination by trace metals in the species Paracentrotus lividus. Biometric analysis, quantification analyses of the elements Cd, Pb, Ni, Fe, Mn, Zn, and Cu, as well as histopathological evaluations were performed in gonads of P. lividus collected from an area affected by hydrocarbons, named as impacted shore (IS) and an area not affected, named reference shore (RS). The results showed that carapace diameter (DC), total wet weight (WW), and Cd concentrations in the gonads were significantly influenced by the interaction between the rocky shores of origin, the months of sampling, and by the sex of the individuals. Moreover, from July until September, the levels of Zn and Cd were significantly lower in male than in female gonads. In July (the month of the oil spill), the indexes of histopathological alterations (IHPA) of membrane dilation were significantly higher in individuals from the IS, compared to the individuals from the RS. In addition, there were significant correlations between biometric variables (wet weight, diameter of carapace, gonadal weight, and gonadosomatic index) and the elements Cd, Cu, Ni, and Mn concentrations. Lastly, a delay in the gametogenic cycle of the sea urchins from IS was also observed. Taken together, these findings suggest that direct exposure to trace metals induces histopathological lesions in P. lividus' gonads and affects its reproductive cycle.

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.

Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve 'active' regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain 'inactive' regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.

Comparison of the Efficiency of Different Eradication Treatments to Minimize the Impacts Caused by the Invasive Tunicate Styela plicata in Mussel Aquaculture.

In 2017, aquaculture producers of the Albufeira lagoon, Portugal, reported an invasion of tunicates that was disrupting mussel production, particularly the tunicate Styela plicata (Lesueur, 1823). A totally effective eradication method still does not exist, particularly for S. plicata, and the effects of the eradication treatments on bivalves' performance are also poorly understood. Our study examined the effectiveness of eradication treatments using three laboratory trials and five treatments (air exposure, freshwater immersion, sodium hypochlorite, hypersaline solution and acetic acid) for S. plicata, as well as their effects on survival and growth of blue mussel Mytilus edulis Linnaeus, 1758. While air exposure and freshwater immersion caused a 27% mortality rate in S. plicata, the acetic acid treatment was the most effective in eliminating this species (>90% mortality). However, a 33-40% mortality rate was registered in mussels. Both species were not affected by the hypersaline treatment in the last trial, but the sodium hypochlorite treatment led to a 57% mortality rate in mussels. Differences in mussels' growth rates were not detected. These trials represent a step forward in responding to the needs of aquaculture producers. However, further studies are needed to investigate the susceptibility of tunicates to treatments according to sexual maturation, as well as to ensure minimum mussel mortality in the most effective treatments, and to better understand the effects on mussel physiological performance in the long-term.

Evaluating sea cucumbers as extractive species for benthic bioremediation in mussel farms.

Filter-feeding mussels blend suspended particles into faeces and pseudo-faeces enhancing organic matter flows between the water column and the bottom, and strengthening benthic-pelagic coupling. Inside operating farms, high bivalve densities in relatively confined areas result in an elevated rate of organic sinking to the seabed, which may cause a localized impact in the immediate surrounding. Deposit-feeding sea cucumbers are potentially optimal candidates to bioremediate mussel organic waste, due to their ability to process organic-enriched sediments impacted by aquaculture waste. However, although the feasibility of this polyculture has been investigated for a few Indo-Pacific species, little is known about Atlanto-Mediterranean species. Hence, for the first time, in the present study, we conducted a comparative investigation on the suitability of different Mediterranean sea cucumber species, to be reared in Integrated Multitrophic Aquaculture (IMTA) with mussels. A pilot-scale experiment was accomplished operating within a mussel farm where two sea cucumbers species, Holothuria tubulosa and Holothuria polii, were caged beneath the long-line mussel farm of Mytilus galloprovincialis. After four months, H. tubulosa showed high survivorship (94%) and positive somatic growth (6.07%); conversely H. polii showed negative growth (- 25.37%), although 92% of specimens survived. Furthermore, sea cucumber growth was size-dependent. In fact, smaller individuals, independently from the species, grew significantly faster than larger ones. These results evidenced a clear difference in the suitability of the two sea cucumber species for IMTA with M. galloprovincialis, probably due to their different trophic ecology (feeding specialization on different microhabitats, i.e. different sediment layers). Specifically, H. tubulosa seems to be an optimal candidate as extractive species both for polycultures production and waste bioremediation in M. galloprovincialis operating farms.

Perfil epidemiológico e dinâmica da distribuição dos acidentes aracdônicos em humanos no estado de São Paulo, 2007-2018

Objetivo: descrever o perfil epidemiológico de acidentes aracdônicos envolvendo humanos e sua dinâmica de distribuição no estado de São Paulo entre2007 a 2018. Método: estudo epidemiológico do tipo descritivo. Foram utilizados dados do Sistema de Informação de Agravos de Notificação, sendo utilizada variáveis relacionadas ao tipo de acidente e caracterização das vítimas. Por meio de estatística descritiva e indicadores de saúde (coeficiente de incidência), obteve-se o diagrama de controle e a distribuição espacial. A população foi obtida pela Fundação Sistema Estadual de Análise de Dados do estado de São Paulo. Resultados: no período estudado, observou-se que, em sua maioria, o gênero das aranhas foi ignorado(53,3%). Dos gêneros identificados, a Phoneutria apresentou maior prevalência(18,9%), sendo as mãos / dedos das mãos os seguimentos mais acometimento (38,0%). A maioria dos acidentes envolveu homens (60,1%), entre 20 a 59 anos de idade(59,6%) e residentes da zona urbana (49,5%). Quase 50% dos casos confirmados não informaram a escolaridade e menos de 1% da amostra era gestante. O diagrama de controle revelou uma estimativa de epidemia entre setembro e dezembro de 2018 e os meses com maiores registros correspondem ao verão. Os municípios que apresentaram maiores índices se localizaram entre as regiões nordeste e sudoeste doestado, sendo Campo Limpo Paulista o município com maior estimativa do coeficiente de incidência. Conclusão: houve alta incidência nos municípios do estado estudado que se situaram em regiões de Floresta Ombrófila Densa. Por isso, sugere-se que essas regiões tenham maior monitoramento à cerca desses acidentes.

Reproductive Biology of the Sea Cucumber Holothuria mammata (Echinodermata: Holothuroidea).

Holothuria mammata is one of the most valuable species of sea cucumber, as well as one of the main target species harvested in the Mediterranean and NE-Atlantic regions. This study aims to describe the reproductive cycle of H. mammata in a coastal area of southwest Portugal. Monthly samplings were carried out for 19 months, with the concomitant collection of environmental data and biometric data. H. mammata had a sex ratio of 1:1.2 (male:female) and a size at first maturity of 142 mm for males and 167 mm for females. The gonadosomatic index (GI) peaked between April and May for both sexes. Gonad development started when days had a shorter photoperiod (9 to 13 h of sunlight) and lower seawater temperature (<15 °C), and spawning occurred later, with longer photoperiod (13 to 15 h of sunlight) and higher seawater temperature (>15 °C) and chlorophyll-a concentrations. The development of new studies to increase the biological and ecological knowledge of the populations of H. mammata is essential to create conditions for the domestication of broodstock in captivity, to allow the development of fishing regulations based on informed decisions and to create precise measures for the conservation of ecosystems.

Altered nuclear architecture in blood cells from Huntington's disease patients.

BACKGROUND: Cell nuclear architecture has been explored in cancer and laminopathies but not in neurodegenerative disorders. Huntington's disease (HD) is a neurodegenerative disorder that leads to neuronal death. Chromosome-wide changes in gene expression have been reported in HD, not only in the brain but also in peripheral blood cells, but whether this translates into nuclear and chromosome architecture alterations has not yet been studied. METHODS: We investigate nuclear structure and chromosome organization in HD blood cells using fluorescence in situ hybridization in ultrathin cryosections (cryoFISH), coupled with machine learning image analysis to evaluate size, distribution, and morphology of nuclei and chromosomes. Four chromosomes were analyzed based on up- or downregulation of gene expression in HD. RESULTS: We show that blood cells from HD patients display increased nuclear size and filamentary shape, increased size of gene-rich chromosome 19, decreased filamentary shape of gene-rich chromosome 22, and a more radially centralized position for chromosome 19, whereas chromosomes 4 and 5 do not show detectable differences. CONCLUSIONS: We identify gross changes in nuclear architecture and chromosome organization associated with HD in blood. This adds a new layer of information onto disrupting mechanisms in HD and increases the potential of using blood to survey HD.

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.

DNA accessibility of cis-regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many genes regulating embryonic development have been identified, the underlying CRE dynamics controlling their expression remain largely uncharacterized. To address this, we produced a multimodal resource and genomic regulatory map for the zebrafish community, which integrates single-cell combinatorial indexing assay for transposase-accessible chromatin with high-throughput sequencing (sci-ATAC-seq) with bulk histone PTMs and Hi-C data to achieve a genome-wide classification of the regulatory architecture determining transcriptional activity in the 24-h post-fertilization (hpf) embryo. We characterized the genome-wide chromatin architecture at bulk and single-cell resolution, applying sci-ATAC-seq on whole 24-hpf stage zebrafish embryos, generating accessibility profiles for ∼23,000 single nuclei. We developed a genome segmentation method, ScregSeg (single-cell regulatory landscape segmentation), for defining regulatory programs, and candidate CREs, specific to one or more cell types. We integrated the ScregSeg output with bulk measurements for histone post-translational modifications and 3D genome organization and identified new regulatory principles between chromatin modalities prevalent during zebrafish development. Sci-ATAC-seq profiling of npas4l/cloche mutant embryos identified novel cellular roles for this hematovascular transcriptional master regulator and suggests an intricate mechanism regulating its expression. Our work defines regulatory architecture and principles in the zebrafish embryo and establishes a resource of cell-type-specific genome-wide regulatory annotations and candidate CREs, providing a valuable open resource for genomics, developmental, molecular, and computational biology.

Cell-type specialization is encoded by specific chromatin topologies.

The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1-3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi4-6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.

Potential use of macroalgae Gracilaria gracilis in diets for European seabass (Dicentrarchus labrax): Health benefits from a sustainable source.

Seaweeds still possess a large undisclosed potential, mainly due to their constituent's richness, which may have several uses for society. In aquaculture, they may play a role as an ecological sustainable aquafeed supplement to increase overall health and fight pathogenic outbreaks. This study aimed to evaluate the general health modulation that the inclusion of Gracilaria gracilis could accomplish in the diet of Dicentrarchus labrax. Dried algae at 2.5% and 5% and algal extract at 0.35% inclusion levels were supplemented to seabass diet to evaluate possible growth, haematological, immunological, antioxidant, metabolic, and intestinal morphological modulations. The supplementations did not impact growth or feed utilization, and barely affected the haematological profile and some metabolic parameters. Nevertheless, it caused a marked outcome on lysozyme, some oxidative stress biomarkers, and intestine morphology, suggesting beneficial consequences from the algal inclusion. Dried algae powder, with a 2.5% inclusion, boosted immune response, with higher plasmatic lysozyme and intestinal acid goblet cells and protected against oxidative damages by improved enzymatic and non-enzymatic responses. Thus, we provide evidence that dietary seaweed application may be a path towards a more sustainable aquaculture industry.

Aedes aegypti: egg morphology and embryonic development.

BACKGROUND: The diseases for which Aedes aegypti is a vector are worrisome. The high vector competence of this mosquito, as well as its anthropophilia and ability to adapt to the urban environment, allows it to exploit many habitats, making its prevention an arduous task. Despite current disease control measures focused on the mosquito, the effectiveness in containing its dispersion still requires improvement; thus greater knowledge about this insect is fundamental. METHODS: Aedes aegypti egg morphology and embryonic development were analyzed from eggs of the insectary of the Institute of Biomedical Sciences of the University of São Paulo. Optical (light and confocal) and electronic (transmission and scanning) microscopy were used to analyze the morphological and ultrastructural features of the eggs. Embryos were observed in the initial (0-20.5 h after egg-laying), intermediate (20.6-40.1 h after egg-laying), and final (40.2-61.6 h) stages of development, and kept at a temperature of 28 °C ± 1 °C until collection for processing. RESULTS: Eggs of Ae. aegypti were whitish at the time of oviposition, and then quickly became black. The egg length was 581.45 ± 39.73 µm and the width was 175.36 ± 11.59. Access to the embryo was difficult due to the egg morphology, point of embryonic development, and difficult permeability of the exochorion (mainly in fixation). Only about 5% of the collected eggs were successfully processed. In the initial stage of embryonic development, characteristics suggestive of intense cellular activity were found. In the intermediate stage, the beginning of the segmentation process was evident. In the final phase, it was possible to differentiate the cephalic region and the thoracic and abdominal segments. CONCLUSION: The chorion was found to be an important protective barrier and a limiting factor for the evaluation of the embryos and mosquito embryonic cells, indicating that further studies need to be carried out to identify the reason that this occurs.

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.

Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. The minimal number of cells required in replicate experiments to return statistically similar contacts is different across the technologies, being lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal levels follow an inverse power law with detection efficiency and grow with genomic distance differently among the three methods, being lowest in GAM for genomic separations >1 Mb.

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.

MOTIVATION: Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM's ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a priori. So far, however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes. RESULTS: We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimize phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data. AVAILABILITY AND IMPLEMENTATION: GAMIBHEAR is available as an R package under the open-source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.