scholarly journals The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures

2019 ◽  
Author(s):  
Ningbo Chen ◽  
Weiwei Fu ◽  
Jianbang Zhao ◽  
Jiafei Shen ◽  
Qiuming Chen ◽  
...  
Keyword(s):  
Bovine Genome ◽  
Distribution Patterns ◽  
Global Scale ◽  
Genomic Region ◽  
Genome Browser ◽  
Web Database ◽  
Genome Variation ◽  
Gene Search ◽  
Variation Database ◽  
Coordinate Conversion

AbstractNext-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.

scholarly journals Global biogeography of living brachiopods: Bioregionalization patterns and possible controls

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259004
Author(s):  
Facheng Ye ◽  
G. R. Shi ◽  
Maria Aleksandra Bitner
Keyword(s):  
Large Scale ◽  
Coastal Upwelling ◽  
Seawater Temperature ◽  
Regional Scale ◽  
Distribution Patterns ◽  
Global Scale ◽  
Biodiversity Hotspots ◽  
Network Analyses ◽  
Ocean Gyres ◽  
Ecological Variable

The global distribution patterns of 14918 geo-referenced occurrences from 394 living brachiopod species were mapped in 5° grid cells, which enabled the visualization and delineation of distinct bioregions and biodiversity hotspots. Further investigation using cluster and network analyses allowed us to propose the first systematically and quantitatively recognized global bioregionalization framework for living brachiopods, consisting of five bioregions and thirteen bioprovinces. No single environmental or ecological variable is accountable for the newly proposed global bioregionalization patterns of living brachiopods. Instead, the combined effects of large-scale ocean gyres, climatic zonation as well as some geohistorical factors (e.g., formation of land bridges and geological recent closure of ancient seaways) are considered as the main drivers at the global scale. At the regional scale, however, the faunal composition, diversity and biogeographical differentiation appear to be mainly controlled by seawater temperature variation, regional ocean currents and coastal upwelling systems.

scholarly journals The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

2017 ◽  
Author(s):  
Yanli Wang ◽  
Bo Zhang ◽  
Lijun Zhang ◽  
Lin An ◽  
Jie Xu ◽  
...  
Keyword(s):  
Genome Organization ◽  
Target Genes ◽  
Genome Structure ◽  
Regulatory Elements ◽  
Genomic Region ◽  
Genome Browser ◽  
Chromatin Interaction ◽  
Interaction Data ◽  
3D Genome ◽  
Chromatin Interactions

ABSTRACTRecent advent of 3C-based technologies such as Hi-C and ChIA-PET provides us an opportunity to explore chromatin interactions and 3D genome organization in an unprecedented scale and resolution. However, it remains a challenge to visualize chromatin interaction data due to its size and complexity. Here, we introduce the 3D Genome Browser (http://3dgenome.org), which allows users to conveniently explore both publicly available and their own chromatin interaction data. Users can also seamlessly integrate other “omics” data sets, such as ChIP-Seq and RNA-Seq for the same genomic region, to gain a complete view of both regulatory landscape and 3D genome structure for any given gene. Finally, our browser provides multiple methods to link distal cis-regulatory elements with their potential target genes, including virtual 4C, ChIA-PET, Capture Hi-C and cross-cell-type correlation of proximal and distal DNA hypersensitive sites, and therefore represents a valuable resource for the study of gene regulation in mammalian genomes.

scholarly journals Diatoms Are Selective Segregators in Global Ocean Planktonic Communities

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Flora Vincent ◽  
Chris Bowler
Keyword(s):  
Open Access ◽  
Large Scale ◽  
Abiotic Factors ◽  
Biotic Interactions ◽  
Distribution Patterns ◽  
Global Scale ◽  
Global Ocean ◽  
Extensive Literature ◽  
Microbial Association ◽  
Species Specific

ABSTRACT Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups. IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.

Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

Genome ◽  
2009 ◽  
Vol 52 (10) ◽  
pp. 862-875 ◽  
Author(s):  
Hong Guo ◽  
Sheng Sun ◽  
Bertrand Eardly ◽  
Turlough Finan ◽  
Jianping Xu
Keyword(s):  
Genome Size ◽  
Sinorhizobium Meliloti ◽  
Distribution Patterns ◽  
Pulse Field ◽  
Size Difference ◽  
Whole Genome ◽  
Nitrogen Fixing ◽  
Genome Variation ◽  
Pulse Field Gel Electrophoresis ◽  
A Genome

Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti , using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45–7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.

RELATIONSHIPS AND DIVERGENCE PATTERNS IN HYPOPTERYGIUM ‘ROTULATUM’ S.L. (HYPOPTERYGIACEAE, BRYOPSIDA) INFERRED FROM trnL INTRON SEQUENCES. STUDIES IN AUSTRAL TEMPERATE RAIN FOREST BRYOPHYTES 7

2000 ◽  
Vol 57 (2) ◽  
pp. 291-307 ◽  
Author(s):  
T. PFEIFFER
Keyword(s):  
New Zealand ◽  
Rain Forest ◽  
Latitudinal Gradient ◽  
Distribution Patterns ◽  
Distinct Species ◽  
Global Scale ◽  
Trnl Intron ◽  
Temperate Rain Forest ◽  
Morphological Species ◽  
Relationship Of

The phylogenetic relationship of species within the Hypopterygium ‘rotulatum’ (Hedw.) Brid. s.l. complex is analysed by sequencing the trnL intron of cp DNA. Furthermore, the divergence in variable New Zealand H. ‘rotulatum’ samples is investigated along a latitudinal gradient. The presented data strongly support the delimitation of at least two distinct species within Hypopterygium ‘rotulatum’ s.l. in New Zealand, Australia and Tasmania, which correspond with the morphological species H. muelleri Hampe (possibly conspecific with H. debile Reichardt) and H. didictyon Müll. Hal., a species known from Chile. The distribution patterns of these species are discussed on a regional (New Zealand) and global scale; indicating an australasian distribution pattern of H. muelleri and a palaeoaustral pattern of H. didictyon.

scholarly journals Genes versus environment: geography and phylogenetic relationships shape the chemical profiles of stingless bees on a global scale

2013 ◽  
Vol 280 (1762) ◽  
pp. 20130680 ◽  
Author(s):  
Sara D. Leonhardt ◽  
Claus Rasmussen ◽  
Thomas Schmitt
Keyword(s):  
Stingless Bees ◽  
Genetic Relatedness ◽  
Distribution Patterns ◽  
Sympatric Species ◽  
Global Scale ◽  
The Body ◽  
Allopatric Species ◽  
Chemical Profiles ◽  
Highly Correlated ◽  
Genetically Determined

Chemical compounds are highly important in the ecology of animals. In social insects, compounds on the body surface represent a particularly interesting trait, because they comprise different compound classes that are involved in different functions, such as communication, recognition and protection, all of which can be differentially affected by evolutionary processes. Here, we investigate the widely unknown and possibly antagonistic influence of phylogenetic and environmental factors on the composition of the cuticular chemistry of tropical stingless bees. We chose stingless bees because some species are unique in expressing not only self-produced compounds, but also compounds that are taken up from the environment. By relating the cuticular chemistry of 40 bee species from all over the world to their molecular phylogeny and geographical occurrence, we found that distribution patterns of different groups of compounds were differentially affected by genetic relatedness and biogeography. The ability to acquire environmental compounds was, for example, highly correlated with the bees' phylogeny and predominated in evolutionarily derived species. Owing to the presence of environmentally derived compounds, those species further expressed a higher chemical and thus functional diversity. In Old World species, chemical similarity of both environmentally derived and self-produced compounds was particularly high among sympatric species, even when they were less related to each other than to allopatric species, revealing a strong environmental effect even on largely genetically determined compounds. Thus, our findings do not only reveal an unexpectedly strong influence of the environment on the cuticular chemistry of stingless bees, but also demonstrate that even within one morphological trait (an insect's cuticular profile), different components (compound classes) can be differentially affected by different drivers (relatedness and biogeography), depending on the functional context.

scholarly journals WGVD: an integrated web-database for wheat genome variation and selective signatures

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Jierong Wang ◽  
Weiwei Fu ◽  
Rui Wang ◽  
Dexiang Hu ◽  
Hong Cheng ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Genome ◽  
Wheat Genome ◽  
Exome Capture ◽  
Whole Genome ◽  
Web Database ◽  
Genome Resequencing ◽  
Genome Variation ◽  
Genomic Variations ◽  
Whole Genome Resequencing

Abstract Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding. Database URL http://animal.nwsuaf.edu.cn/code/index.php/Wheat

Sign in / Sign up

Export Citation Format

Share Document