scholarly journals A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombina and B. variegata)

2021 ◽  
Author(s):  
Beate Nürnberger ◽  
Stuart J E Baird ◽  
Dagmar Čížková ◽  
Anna Bryjová ◽  
Austin B Mudd ◽  
...  
Keyword(s):  
Large Scale ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Hybrid Zones ◽  
Chromosome 5 ◽  
Draft Genome Assembly ◽  
Novel Approach ◽  
Bombina Bombina

Abstract Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here we report the development of such a map for the hybridising toads, Bombina bombina and B. variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7-10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the non-repetitive portion of the genome that report B. bombina vs. B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4,755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

scholarly journals A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombina and B. variegata)

2020 ◽  
Author(s):  
Beate Nürnberger ◽  
Stuart J.E. Baird ◽  
Dagmar Čížková ◽  
Anna Bryjová ◽  
Austin B. Mudd ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Large Scale ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Secondary Contact ◽  
Gene Pools ◽  
Hybrid Zones ◽  
Chromosome 5 ◽  
Bombina Bombina

AbstractHybrid zones that result from secondary contact between diverged populations offer unparalleled insight into the genetic architecture of emerging reproductive barriers and so shed light on the process of speciation. Natural selection and recombination jointly determine their dynamics, leading to a range of outcomes from finely fragmented mixtures of the parental genomes that facilitate introgression to a situation where strong selection against recombinants retains large unrecombined genomic blocks that act as strong barriers to gene flow. In the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae), two anciently diverged and ecologically distinct taxa meet and produce abundant, fertile hybrids. The dense linkage map presented here enables genomic analysis of the selection-recombination balance that keeps the two gene pools from merging into one. We mapped 4,775 newly developed marker loci from bait-enriched genomic libraries in F2 crosses. The enrichment targets were selected from a draft assembly of the B. variegata genome, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Large-scale synteny between Bombina and Xenopus tropicalis supports the resulting linkage map. By assessing the sex of late-stage F2 tadpoles from histological sections, we also identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety, suggestive of an XY sex determination mechanism. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

scholarly journals The First Draft Genome Assembly of Snow Sheep (Ovis nivicola)

2020 ◽  
Vol 12 (8) ◽  
pp. 1330-1336 ◽  
Author(s):  
Maulik Upadhyay ◽  
Andreas Hauser ◽  
Elisabeth Kunz ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Single Copy ◽  
Climatic Conditions ◽  
Draft Genome Assembly ◽  
Sheep Genome ◽  
Long Reads

Abstract The snow sheep, Ovis nivicola, which is endemic to the mountain ranges of northeastern Siberia, are well adapted to the harsh cold climatic conditions of their habitat. In this study, using long reads of Nanopore sequencing technology, whole-genome sequencing, assembly, and gene annotation of a snow sheep were carried out. Additionally, RNA-seq reads from several tissues were also generated to supplement the gene prediction in snow sheep genome. The assembled genome was ∼2.62 Gb in length and was represented by 7,157 scaffolds with N50 of about 2 Mb. The repetitive sequences comprised of 41% of the total genome. BUSCO analysis revealed that the snow sheep assembly contained full-length or partial fragments of 97% of mammalian universal single-copy orthologs (n = 4,104), illustrating the completeness of the assembly. In addition, a total of 20,045 protein-coding sequences were identified using comprehensive gene prediction pipeline. Of which 19,240 (∼96%) sequences were annotated using protein databases. Moreover, homology-based searches and de novo identification detected 1,484 tRNAs; 243 rRNAs; 1,931 snRNAs; and 782 miRNAs in the snow sheep genome. To conclude, we generated the first de novo genome of the snow sheep using long reads; these data are expected to contribute significantly to our understanding related to evolution and adaptation within the Ovis genus.

Green synthesis, characterization of silver sulfide nanoparticles and antibacterial activity evaluation

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Antibacterial Activity ◽  
Large Scale ◽  
Research Work ◽  
Silver Sulfide ◽  
Morphological Properties ◽  
Effective Diameter ◽  
Novel Approach ◽  
Transmission Electron ◽  
Green Route ◽  
Silver Sulfide Nanoparticles

This research work presents a facile and green route for synthesis silver sulfide (Ag2SNPs) nanoparticles from silver nitrate (AgNO3) and sodium sulfide nonahydrate (Na2S.9H2O) in the presence of rosemary leaves aqueous extract at ambient temperature (27 oC). Structural and morphological properties of Ag2SNPs nanoparticles were analyzed by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The surface Plasmon resonance for Ag2SNPs was obtained around 355 nm. Ag2SNPs was spherical in shape with an effective diameter size of 14 nm. Our novel approach represents a promising and effective method to large scale synthesis of eco-friendly antibacterial activity silver sulfide nanoparticles.

scholarly journals Fractional ridge regression: a fast, interpretable reparameterization of ridge regression

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Ariel Rokem ◽  
Kendrick Kay
Keyword(s):  
Ridge Regression ◽  
Large Scale ◽  
Imaging Data ◽  
Regularization Technique ◽  
Large Scale Data ◽  
Novel Approach ◽  
Manual Exploration ◽  
L2 Norm ◽  
Software Implementations ◽  
Brain Imaging Data

Abstract Background Ridge regression is a regularization technique that penalizes the L2-norm of the coefficients in linear regression. One of the challenges of using ridge regression is the need to set a hyperparameter (α) that controls the amount of regularization. Cross-validation is typically used to select the best α from a set of candidates. However, efficient and appropriate selection of α can be challenging. This becomes prohibitive when large amounts of data are analyzed. Because the selected α depends on the scale of the data and correlations across predictors, it is also not straightforwardly interpretable. Results The present work addresses these challenges through a novel approach to ridge regression. We propose to reparameterize ridge regression in terms of the ratio γ between the L2-norms of the regularized and unregularized coefficients. We provide an algorithm that efficiently implements this approach, called fractional ridge regression, as well as open-source software implementations in Python and matlab (https://github.com/nrdg/fracridge). We show that the proposed method is fast and scalable for large-scale data problems. In brain imaging data, we demonstrate that this approach delivers results that are straightforward to interpret and compare across models and datasets. Conclusion Fractional ridge regression has several benefits: the solutions obtained for different γ are guaranteed to vary, guarding against wasted calculations; and automatically span the relevant range of regularization, avoiding the need for arduous manual exploration. These properties make fractional ridge regression particularly suitable for analysis of large complex datasets.

scholarly journals Novel approach for large‐scale monitoring of submerged aquatic vegetation – a nationwide example from Sweden

2021 ◽  
Author(s):  
Silvia Huber ◽  
Lars B. Hansen ◽  
Lisbeth T. Nielsen ◽  
Mikkel L. Rasmussen ◽  
Jonas Sølvsteen ◽  
...  
Keyword(s):  
Large Scale ◽  
Submerged Aquatic Vegetation ◽  
Aquatic Vegetation ◽  
Novel Approach

scholarly journals The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huai-Jun Xue ◽  
Yi-Wei Niu ◽  
Kari A. Segraves ◽  
Rui-E Nie ◽  
Ya-Jing Hao ◽  
...  
Keyword(s):  
Host Plant ◽  
Plant Cell Wall ◽  
Flea Beetle ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Gene Families ◽  
Ecological Speciation ◽  
Secondary Chemistry ◽  
Host Plant Specialization ◽  
Insight Into

Abstract Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far. Results The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. Conclusions The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

scholarly journals Joint regression and learning from pairwise rankings for personalized image aesthetic assessment

2021 ◽  
Author(s):  
Jin Zhou ◽  
Qing Zhang ◽  
Jian-Hao Fan ◽  
Wei Sun ◽  
Wei-Shi Zheng
Keyword(s):  
Large Scale ◽  
Assessment Model ◽  
Generic Model ◽  
Small Subset ◽  
Deep Convolutional Neural Networks ◽  
Personal Taste ◽  
Hinge Loss ◽  
Novel Approach ◽  
Large Scale Dataset ◽  
Image Pairs

AbstractRecent image aesthetic assessment methods have achieved remarkable progress due to the emergence of deep convolutional neural networks (CNNs). However, these methods focus primarily on predicting generally perceived preference of an image, making them usually have limited practicability, since each user may have completely different preferences for the same image. To address this problem, this paper presents a novel approach for predicting personalized image aesthetics that fit an individual user’s personal taste. We achieve this in a coarse to fine manner, by joint regression and learning from pairwise rankings. Specifically, we first collect a small subset of personal images from a user and invite him/her to rank the preference of some randomly sampled image pairs. We then search for the K-nearest neighbors of the personal images within a large-scale dataset labeled with average human aesthetic scores, and use these images as well as the associated scores to train a generic aesthetic assessment model by CNN-based regression. Next, we fine-tune the generic model to accommodate the personal preference by training over the rankings with a pairwise hinge loss. Experiments demonstrate that our method can effectively learn personalized image aesthetic preferences, clearly outperforming state-of-the-art methods. Moreover, we show that the learned personalized image aesthetic benefits a wide variety of applications.

scholarly journals Reservoir-Induced Land Deformation: Case Study from the Grand Ethiopian Renaissance Dam

2021 ◽  
Vol 13 (5) ◽  
pp. 874
Author(s):  
Yu Chen ◽  
Mohamed Ahmed ◽  
Natthachet Tangdamrongsub ◽  
Dorina Murgulet
Keyword(s):  
Land Surface ◽  
Large Scale ◽  
Surface Deformation ◽  
Vertical Displacement ◽  
Nile River ◽  
Reservoir Volume ◽  
Novel Approach ◽  
Land Deformation ◽  
Large Scale Land ◽  
The Impact

The Nile River stretches from south to north throughout the Nile River Basin (NRB) in Northeast Africa. Ethiopia, where the Blue Nile originates, has begun the construction of the Grand Ethiopian Renaissance Dam (GERD), which will be used to generate electricity. However, the impact of the GERD on land deformation caused by significant water relocation has not been rigorously considered in the scientific research. In this study, we develop a novel approach for predicting large-scale land deformation induced by the construction of the GERD reservoir. We also investigate the limitations of using the Gravity Recovery and Climate Experiment Follow On (GRACE-FO) mission to detect GERD-induced land deformation. We simulated three land deformation scenarios related to filling the expected reservoir volume, 70 km3, using 5-, 10-, and 15-year filling scenarios. The results indicated: (i) trends in downward vertical displacement estimated at −17.79 ± 0.02, −8.90 ± 0.09, and −5.94 ± 0.05 mm/year, for the 5-, 10-, and 15-year filling scenarios, respectively; (ii) the western (eastern) parts of the GERD reservoir are estimated to move toward the reservoir’s center by +0.98 ± 0.01 (−0.98 ± 0.01), +0.48 ± 0.00 (−0.48 ± 0.00), and +0.33 ± 0.00 (−0.33 ± 0.00) mm/year, under the 5-, 10- and 15-year filling strategies, respectively; (iii) the northern part of the GERD reservoir is moving southward by +1.28 ± 0.02, +0.64 ± 0.01, and +0.43 ± 0.00 mm/year, while the southern part is moving northward by −3.75 ± 0.04, −1.87 ± 0.02, and −1.25 ± 0.01 mm/year, during the three examined scenarios, respectively; and (iv) the GRACE-FO mission can only detect 15% of the large-scale land deformation produced by the GERD reservoir. Methods and results demonstrated in this study provide insights into possible impacts of reservoir impoundment on land surface deformation, which can be adopted into the GERD project or similar future dam construction plans.

scholarly journals Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Bhavani Manivannan ◽  
Niranjana Mahalingam ◽  
Sudhir Jadhao ◽  
Amrita Mishra ◽  
Pravin Nilawe ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Genome Assembly ◽  
Biofilm Formation ◽  
Draft Genome ◽  
Drug Resistant ◽  
Draft Genome Assembly ◽  
Extensively Drug Resistant ◽  
History Of ◽  
Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

scholarly journals A NOTE ON PHASING LONG GENOMIC REGIONS USING LOCAL HAPLOTYPE PREDICTIONS

2006 ◽  
Vol 04 (03) ◽  
pp. 639-647 ◽  
Author(s):  
ELEAZAR ESKIN ◽  
RODED SHARAN ◽  
ERAN HALPERIN
Keyword(s):  
Large Scale ◽  
Computational Cost ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Novel Approach ◽  
Maximum Likelihood Criterion ◽  
The Common ◽  
Genomic Regions ◽  
High Computational Cost ◽  
Combining Information

The common approaches for haplotype inference from genotype data are targeted toward phasing short genomic regions. Longer regions are often tackled in a heuristic manner, due to the high computational cost. Here, we describe a novel approach for phasing genotypes over long regions, which is based on combining information from local predictions on short, overlapping regions. The phasing is done in a way, which maximizes a natural maximum likelihood criterion. Among other things, this criterion takes into account the physical length between neighboring single nucleotide polymorphisms. The approach is very efficient and is applied to several large scale datasets and is shown to be successful in two recent benchmarking studies (Zaitlen et al., in press; Marchini et al., in preparation). Our method is publicly available via a webserver at .

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