ResearchPad - data-note https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Traumatic childhood events of parents enrolled in the Avon Longitudinal Study of Parents and Children (ALSPAC)]]> https://www.researchpad.co/article/elastic_article_9220 Background: Early life experiences can have a significant impact on an individual’s later behaviour, the way they view the world, their beliefs and their success at forming strong interpersonal relationships. These factors may subsequently influence the way that the individual may parent their children, which in turn may have an effect on their child’s behaviour, mental health and world view. Research has linked early traumatic life experiences in the parent’s childhood to disorganised attachment to their own child. In this paper we describe the data collected from parents enrolled in the Avon Longitudinal Study of Parents and Children (ALSPAC) on traumatic events experienced during their childhood, so that it can act as a resource for researchers in the future when considering outcomes on the adult, their children and grandchildren.

Methods: Data were collected via multiple questionnaires completed by parents enrolled into the ALSPAC study. During pregnancy and post-delivery, questionnaires were administered between 1990 and 1992 via post to the study mothers and their partners. Data were collected on life events including bereavement, sexual abuse, physical abuse, abandonment, neglect, memories of childhood and accidents. Other reports of traumatic events in childhood were reported by parents using free text. This can be made available to researchers for coding on request.

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<![CDATA[Species-level evaluation of the human respiratory microbiome]]> https://www.researchpad.co/article/N78fcfb0f-216d-4cb5-9ea6-0601a1b932eb

Abstract

Background

Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract.

Findings

Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ∼600,000 rRNA reads passing quality assurance/quality control (70–95% identify; >1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (>750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (<5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis.

Conclusions

Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, >100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.

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<![CDATA[The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758]]> https://www.researchpad.co/article/N1028d2a4-023c-4039-9f9f-e5a2d1f33679

We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.

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<![CDATA[The FRAXA and FRAXE allele repeat size of boys from the Avon Longitudinal Study of Parents and Children (ALSPAC)]]> https://www.researchpad.co/article/Nbc159908-7a4b-4f81-a342-72f3b75eae03

The FRAXA and FRAXE alleles of the FMR1 and FMR2 genes located on the X chromosome contain varying numbers of trinucleotide repeats. Large numbers of repeats at FRAXA (full mutations) manifest as Fragile X syndrome, associated with mental impairment that affects males more severely. In this paper, we present the dataset of frequencies of FRAXA and FRAXE repeat size extracted from DNA samples collected from boys enrolled in the Avon Longitudinal Study of Parents and Children (ALSPAC). DNA data were extracted from samples collected in ALSPAC clinics from several types of samples: cord blood, venepuncture blood taken at 43 months, 61 months, seven years or nine years. The DNA was amplified at FRAXA and FRAXE using fluorescent PCR in the Wessex Regional Genetics Laboratory, Salisbury District Hospital. The mean repeat size for FRAXA is 28.92 (S.D. 5.44), the median 30 and the range 8 to 68. There were particularly high numbers of boys with repeat sizes of 20 (10.67%) and 23 (7.35%). The mean repeat size for FRAXE is 17.41 (S.D. 3.94), with median of 16 and range of 0 to 61. There is a relatively high degree of variation of the FRAXA repeat size particularly and we suggest the extensive data available from the ALSPAC study opens up areas of research into understanding phenotypes associated with relatively unexplored repeat sizes. This could be particularly interesting for the lower repeat sizes occurring with high frequency at FRAXA in this population. As the data can be linked to exposures and phenotypes, it will provide a resource for researchers worldwide.

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<![CDATA[Body image of people over 50 in Spain measured using the BSQ test]]> https://www.researchpad.co/article/Nfedbc6d5-b023-481e-b8c4-9c2d5b3f036d

Objectives

To show the body image of people over 50 in Spain using the Body Shape Questionnaire test (BSQ), taking into account attribute variables of great interest such as age, gender, sentimental status, habitat (rural or urban) and the season of the year in which the test is done (winter or summer).

Data description

The results obtained show the current state of the body image of 176 people in the process of ageing in Spain. The data collected from the participants are organised taking into account attribute variables of significant impact on body image such as age, gender, having a stable partner, habitat (rural or urban) and the season of the year in which the test is done (winter or summer). These data are especially useful to show how body image changes over the time, depending on the different attributes and according to diverse emotional and social situations. They can be used in studies on body image, eating disorders or studies that assess the importance of physical appearance in someone’s self-esteem regardless of age group, geographic area or personal emotional circumstances.

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<![CDATA[Maternal survival in a low-resource setting, Mpilo Central Hospital, Bulawayo, Zimbabwe]]> https://www.researchpad.co/article/N1b9b1dca-8102-476b-80c9-e2e1ab0c2014

Objectives

Maternal mortality is an important global subject. This dataset was generated from a retrospective cross-sectional study carried out at Mpilo Central Hospital, covering the period January 1, 2015 to December 31, 2018. The aim of the study was to compare how frequently the exposure to a risk factor was related to maternal death. Maternal deaths that were recorded during the study period were considered as cases. Controls were selected randomly from women of child-bearing age who survived during the study period. Low-resourced countries contribute significantly to global maternal deaths. Understanding risk factors could help reduce maternal mortality.

Data description

The dataset contains data of 387 pregnant women who were included in the study. Data were collected as secondary data using a data collection sheet, as recorded by the hospital staff that gave all necessary demographic details in birth and mortality registers. The data collected included socio-demographic and clinical data. The independent variables were maternal age, gravidity, parity, antenatal visits, booking status, marital status, educational status, days spent in hospital, mode of delivery, fetal outcomes, and maternal complications. The dependent variable was maternal mortality. The data can be used to determine the relationship between the independent variables and maternal death.

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<![CDATA[High-coverage genomes to elucidate the evolution of penguins]]> https://www.researchpad.co/article/N2c6af03d-6a9c-4292-b3ad-5f8fe12e7528

Abstract

Background

Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes.

Results

Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species.

Conclusions

We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.

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<![CDATA[Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)]]> https://www.researchpad.co/article/N45f394d9-71a5-4a7d-9cf0-0ed947f0792b

Abstract

Background

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same “Bartlett” reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis.

Findings

A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

Conclusions

We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.

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<![CDATA[A multi-day and multi-band dataset for a steady-state visual-evoked potential–based brain-computer interface]]> https://www.researchpad.co/article/N75b5336d-de8d-42b3-baa9-24d7ae48592d

Abstract

Background

A steady-state visual-evoked potential (SSVEP) is a brain response to visual stimuli modulated at certain frequencies; it has been widely used in electroencephalography (EEG)-based brain–computer interface research. However, there are few published SSVEP datasets for brain–computer interface. In this study, we obtained a new SSVEP dataset based on measurements from 30 participants, performed on 2 days; our dataset complements existing SSVEP datasets: (i) multi-band SSVEP datasets are provided, and all 3 possible frequency bands (low, middle, and high) were used for SSVEP stimulation; (ii) multi-day datasets are included; and (iii) the EEG datasets include simultaneously obtained physiological measurements, such as respiration, electrocardiography, electromyography, and head motion (accelerator).

Findings

To validate our dataset, we estimated the spectral powers and classification performance for the EEG (SSVEP) datasets and created an example plot to visualize the physiological time-series data. Strong SSVEP responses were observed at stimulation frequencies, and the mean classification performance of the middle frequency band was significantly higher than the low- and high-frequency bands. Other physiological data also showed reasonable results.

Conclusions

Our multi-band, multi-day SSVEP datasets can be used to optimize stimulation frequencies because they enable simultaneous investigation of the characteristics of the SSVEPs evoked in each of the 3 frequency bands, and solve session-to-session (day-to-day) transfer problems by enabling investigation of the non-stationarity of SSVEPs measured on different days. Additionally, auxiliary physiological data can be used to explore the relationship between SSVEP characteristics and physiological conditions, providing useful information for optimizing experimental paradigms to achieve high performance.

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<![CDATA[Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae]]> https://www.researchpad.co/article/5ca26012d5eed0c4846d8a39

Abstract

Background

The barred knifejaw (Oplegnathus fasciatus), a member of the Oplegnathidae family of the Centrarchiformes, is a commercially important rocky reef fish native to East Asia. Oplegnathus fasciatus has become an important fishery resource for offshore cage aquaculture and fish stocking of marine ranching in China, Japan, and Korea. Recently, sexual dimorphism in growth with neo-sex chromosome and widespread biotic diseases in O. fasciatus have been increasing concern in the industry. However, adequate genome resources for gaining insight into sex-determining mechanisms and establishing genetically resistant breeding systems for O. fasciatus are lacking. Here, we analyzed the entire genome of a female O. fasciatus fish using long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly.

Findings

We assembled the O. fasciatus genome with a total of 245.0 Gb of raw reads that were generated using both Pacific Bioscience (PacBio) Sequel and Illumina HiSeq 2000 platforms. The final draft genome assembly was approximately 778.7 Mb, which reached a high level of continuity with a contig N50 of 2.1 Mb. The genome size was consistent with the estimated genome size (777.5 Mb) based on k-mer analysis. We combined Hi-C data with a draft genome assembly to generate chromosome-length scaffolds. Twenty-four scaffolds corresponding to the 24 chromosomes were assembled to a final size of 768.8 Mb with a contig N50 of 2.1 Mb and a scaffold N50 of 33.5 Mb using 1,372 contigs. The identified repeat sequences accounted for 33.9% of the entire genome, and 24 003 protein-coding genes with an average of 10.1 exons per gene were annotated using de novo methods, with RNA sequencing data and homologies to other teleosts. According to phylogenetic analysis using protein-coding genes, O. fasciatus is closely related to Larimichthys crocea, with O. fasciatus diverging from their common ancestor approximately 70.5–88.5 million years ago.

Conclusions

We generated a high-quality draft genome for O. fasciatus using long-read PacBio sequencing technology, which represents the first chromosome-level reference genome for Oplegnathidae species. Assembly of this genome assists research into fish sex-determining mechanisms and can serve as a resource for accelerating genome-assisted improvements in resistant breeding systems.

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<![CDATA[Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water]]> https://www.researchpad.co/article/5c929a58d5eed0c484381e92

Objectives

Enterococci are Gram-positive lactic acid bacteria and common inhabitants of the gastrointestinal tract of mammals, including humans. They are also widely distributed in diverse environments such as soil, water, vegetables and food. Enterococcus faecium is able to produce antimicrobial compounds (enterocins) and thus can act as a probiotic. E. faecium SP15 is a newly identified enterocin-producing strain from spring water that has been subjected to genome sequence analysis to provide understanding of its antimicrobial and probiotic properties.

Data description

The draft genome of E. faecium SP15 comprises of 2,783,033 bp with a G+C content of 38.08%. Five genetic loci predicted to specify enterocin production were identified, but no virulence factors could be detected and only two potential antibiotic resistance genes were noted.

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<![CDATA[Bangladesh Chars Tobacco Assessment Project (CTAP) 2018: a data note]]> https://www.researchpad.co/article/5c33d239d5eed0c4845de170

Objectives

The Chars Tobacco Assessment Project 2018 is a holistic survey conducted in the chars (riverine islands) of Gaibandha in Northern Bangladesh, covering 985 households over 24 clusters. The survey was conducted with two objectives: (1) to assess levels of tobacco consumption and evaluate prevailing socio-economic, behavioral and health status of the chars population, and (2) to look at the effectiveness of advocacy campaigns to reduce tobacco consumption through behavioral nudges via randomized controlled trials (RCTs) in rural Bangladesh. The study site was purposively chosen due to its high tobacco consumption rate, and the geographical segregation of the chars aided in reducing spillovers for RCT design.

Data description

In addition to detailed information on tobacco (smoking and smokeless) consumption and perception, data was collected on: household composition, housing and plot ownership, consumption, risks and shocks coping, dowry, farm production, loans, savings and lending, labor income, asset holdings, migration and remittance, anthropometry, respiratory diseases, co-morbidities, reproductive history, risk and time preference. Unique to the dataset are carbon monoxide readings for accurate short term smoking measurement and FEV1 and PEF values for identification of long term lung damage. The data is representative only for the chars of Gaibandha.

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<![CDATA[Mitochondrial DNA copy number in affected and unaffected LHON mutation carriers]]> https://www.researchpad.co/article/5c33d284d5eed0c4845df6df

Objectives

Leber’s hereditary optic neuropathy (LHON) is a mitochondrial genetic disease characterized by a variable and reduced penetrance. Individuals carrying a primary LHON-causing mitochondrial DNA (mtDNA) mutation may either remain asymptomatic lifelong, as unaffected carriers, or develop sudden central visual loss that rapidly aggravates over some weeks. Over the years several genetic/environmental triggers able to modulate the risk of developing LHON have been proposed. We provided data supporting a possible correlation between LHON penetrance and the mtDNA copy number, a raw index of mitochondrial mass, whose increase could represent a compensatory response that cells implement to alleviate the pathogenic effect of the primary LHON-causing mtDNA mutations.

Data description

We collected Italian and Spanish subjects harboring one of the three common LHON primary mutations, either in heteroplasmic or homoplasmic status. For each population we were able to discriminate between affected subjects presenting typical clinical tracts of LHON and LHON-causing mutation carriers showing no symptoms correlated with vision loss. Each subject has been characterized for the presence of a LHON primary mutation, for its status of homoplasmy or heteroplasmy, and for the mtDNA content per cell, expressed as relative mtDNA/nDNA ratio respect to controls. Additional clinical information is present for all the Italian subjects.

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<![CDATA[Adverse childhood experiences in the children of the Avon Longitudinal Study of Parents and Children (ALSPAC)]]> https://www.researchpad.co/article/5c22c680d5eed0c484aa00b0

Background: Exposure to adverse childhood experiences (ACEs) is a risk factor for poor later life health. Here, we describe the ACE variables measured in the children of the Avon Longitudinal Study of Parents and Children (ALSPAC) study, and a method used to derive summary measures and deal with missing data in them.   

Methods: The ALSPAC data catalogue (59 608 variables) was searched in September 2017 for measures on adversity exposure between birth and 18 years. 6140 adversity questions were then screened for conforming to our ACE definitions and suitability for dichotomisation. This screening identified 541 questions on ten ‘classic’ ACEs (sexual, physical or emotional abuse, emotional neglect, substance abuse by the parents, parental mental illness or suicide attempt, violence between parents, parental separation, bullying and parental criminal conviction) and nine additional ACEs (bond between parent and child, satisfaction with neighbourhood, social support for the parent, social support for the child, physical illness of a parent, physical illness of the child, financial difficulties, low social class and violence between child and partner). These were used to derive a binary construct for exposure to each ACE. Finally, as cumulative measures of childhood adversity, different combinations of the 19 ACE constructs were summed to give total adversity scores. An appropriate strategy for multiple imputation was developed to deal with the complex patterns of missing data.

Results: The ACE constructs and ACE-scores for exposure between birth and 16 years had prevalence estimates that were comparable to previous reports (for instance 4% sexual abuse, 18% physical abuse, 25% bullied, 32% parental separation).

Conclusions: ACE constructs, derived using a pragmatic approach to handle the high dimensional ALSPAC data, can be used in future analyses on childhood adversity in ALSPAC children.

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<![CDATA[Head models of healthy and depressed adults for simulating the electric fields of non-invasive electric brain stimulation]]> https://www.researchpad.co/article/5c15fb57d5eed0c4842f3418

During the past decade, it became clear that the electric field elicited by non-invasive brain stimulation (NIBS) techniques such as transcranial direct current stimulation (tDCS) and transcranial magnetic stimulation (TMS) are substantially influenced by variations in individual head and brain anatomy. In addition to structural variations in the healthy, several psychiatric disorders are characterized by anatomical alterations that are likely to further constrain the intracerebral effects of NIBS. Here, we present high-resolution realistic head models derived from structural magnetic resonance imaging data of 19 healthy adults and 19 patients diagnosed with major depressive disorder (MDD). By using a freely available software package for modelling the electric fields induced by different NIBS protocols, we show that our head models are well-suited for assessing inter-individual and between-group variability in the magnitude and focality of tDCS-induced electric fields for two protocols targeting the left dorsolateral prefrontal cortex.

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<![CDATA[Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines]]> https://www.researchpad.co/article/5c11fc25d5eed0c48483be5e

Abstract

Background

Gene fusions derive from chromosomal rearrangements. The resulting chimeric transcripts are often endowed with oncogenic potential. Furthermore, they serve as diagnostic tools for the clinical classification of cancer subgroups with different prognosis and, in some cases, they can provide specific drug targets. To date, many efforts have been carried out to study gene fusion events occurring in tumor samples. In recent years, the availability of a comprehensive next-generation sequencing dataset for all existing human tumor cell lines has provided the opportunity to further investigate these data in order to identify novel and still uncharacterized gene fusion events.

Results

In our work, we have extensively reanalyzed 935 paired-end RNA-sequencing experiments downloaded from the Cancer Cell Line Encyclopedia repository, aiming at addressing novel putative cell-line specific gene fusion events in human malignancies. The bioinformatics analysis has been performed by the execution of four gene fusion detection algorithms. The results have been further prioritized by running a Bayesian classifier that makes an in silico validation. The collection of fusion events supported by all of the predictive software results in a robust set of ∼1,700 in silico predicted novel candidates suitable for downstream analyses. Given the huge amount of data and information produced, computational results have been systematized in a database named LiGeA. The database can be browsed through a dynamic and interactive web portal, further integrated with validated data from other well-known repositories. Taking advantage of the intuitive query forms, the users can easily access, navigate, filter, and select the putative gene fusions for further validations and studies. They can also find suitable experimental models for a given fusion of interest.

Conclusions

We believe that the LiGeA resource can represent not only the first compendium of both known and putative novel gene fusion events in the catalog of all of the human malignant cell lines but it can also become a handy starting point for wet-lab biologists who wish to investigate novel cancer biomarkers and specific drug targets.

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<![CDATA[Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data]]> https://www.researchpad.co/article/5c1161c1d5eed0c48463a5ac

Objectives

Mammalian genomics studies, especially those focusing on transcriptional regulation, require information on genomic locations of regulatory regions, particularly, transcription factor (TF) binding sites. There are plenty of published ChIP-Seq data on in vivo binding of transcription factors in different cell types and conditions. However, handling of thousands of separate data sets is often impractical and it is desirable to have a single global map of genomic regions potentially bound by a particular TF in any of studied cell types and conditions.

Data description

Here we report human and mouse cistromes, the maps of genomic regions that are routinely identified as TF binding sites, organized by TF. We provide cistromes for 349 mouse and 599 human TFs. Given a TF, its cistrome regions are supported by evidence from several ChIP-Seq experiments or several computational tools, and, as an optional filter, contain occurrences of sequence motifs recognized by the TF. Using the cistrome, we provide an annotation of TF binding sites in the vicinity of human and mouse transcription start sites. This information is useful for selecting potential gene targets of transcription factors and detecting co-regulated genes in differential gene expression data.

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<![CDATA[Genome sequence of the brown rot fungal pathogen Monilinia fructigena]]> https://www.researchpad.co/article/5c1161ced5eed0c48463a849

Objectives

Monilinia fructigena (phylum Ascomycota, family Sclerotiniaceae) is a plant pathogen that causes brown rot and blossom blight in pome fruit and stone fruit of the Rosaceae family, which can cause significant losses in the field and mainly postharvest. The aim of this study was to create a high-quality draft of the M. fructigena genome assembly and annotation that provides better understanding of the epidemiology of the pathogen and its interactions with the host(s) and will thus improve brown rot management.

Data description

We report here on the genome sequence of M. fructigena strain Mfrg269 that was collected from plum in southern Italy. This is assembled into 131 scaffolds, with a total size of 43.125 Mb, with 9960 unique protein-coding genes. The novel genomic resources allow improved genomic comparisons among the most important pathogens belonging to the Monilinia genus, with the aim being to improve the knowledge of their plant–pathogen interactions, population biology, and control.

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<![CDATA[Genomes and virulence difference between two physiological races of Phytophthora nicotianae]]> https://www.researchpad.co/article/5989da4aab0ee8fa60b8ca1f

Background

Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, races 0 and 1, are predominantly observed in cultivated tobacco fields around the world. Race 0 has been reported to be more aggressive, having a shorter incubation period, and causing worse root rot symptoms, while race 1 causes more severe necrosis. The molecular mechanisms underlying the difference in virulence between race 0 and 1 remain elusive.

Findings

We assembled and annotated the genomes of P. nicotianae races 0 and 1, which were obtained by a combination of PacBio single-molecular real-time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis revealed a highly expanded ATP-binding cassette transporter gene family in P. nicotianae. Specifically, more RxLR effector genes were found in the genome of race 0 than in that of race 1. In addition, RxLR effector genes were found to be mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome.

Conclusions

These results provide not only high quality reference genomes of P. nicotianae, but also insights into the infection mechanisms of P. nicotianae and its co-evolution with the host plant. They also reveal insights into the difference in virulence between the two physiological races.

Electronic supplementary material

The online version of this article (doi:10.1186/s13742-016-0108-7) contains supplementary material, which is available to authorized users.

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<![CDATA[A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum]]> https://www.researchpad.co/article/5989db25ab0ee8fa60bd025a

Background

Tuber melanosporum, also known in the gastronomic community as “truffle”, features one of the largest fungal genomes (125 Mb) with an exceptionally high transposable element (TE) and repetitive DNA content (>58%). The main purpose of DNA methylation in fungi is TE silencing. As obligate outcrossing organisms, truffles are bound to a sexual mode of propagation, which together with TEs is thought to represent a major force driving the evolution of DNA methylation. Thus, it was of interest to examine if and how T. melanosporum exploits DNA methylation to maintain genome integrity.

Findings

We performed whole-genome DNA bisulfite sequencing and mRNA sequencing on different developmental stages of T. melanosporum; namely, fruitbody (“truffle”), free-living mycelium and ectomycorrhiza. The data revealed a high rate of cytosine methylation (>44%), selectively targeting TEs rather than genes with a strong preference for CpG sites. Whole genome DNA sequencing uncovered multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs, almost exclusively in free-living mycelium propagated in vitro. Treatment of mycelia with 5-azacytidine partially reduced DNA methylation and increased TE transcription. Our transcriptome assembly also resulted in the identification of a set of novel transcripts from 614 genes.

Conclusions

The datasets presented here provide valuable and comprehensive (epi)genomic information that can be of interest for evolutionary genomics studies of multicellular (filamentous) fungi, in particular Ascomycetes belonging to the subphylum, Pezizomycotina. Evidence derived from comparative methylome and transcriptome analyses indicates that a non-exhaustive and partly reversible methylation process operates in truffles.

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