scholarly journals Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

2020 ◽  
Vol 49 (D1) ◽  
pp. D1452-D1463 ◽  
Author(s):  
Marcela K Tello-Ruiz ◽  
Sushma Naithani ◽  
Parul Gupta ◽  
Andrew Olson ◽  
Sharon Wei ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Function Annotation ◽  
Functional Annotations ◽  
Pathway Data ◽  
Annotation Information ◽  
Gene Structures ◽  
Functional Analyses ◽  
Function Information ◽  
Reference Genomes ◽  
Pathway Networks

Abstract Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes—over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene–gene interactions. Gramene integrates ontology-based protein structure–function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.

scholarly journals Contrasting genome dynamics between domesticated and wild yeasts

2016 ◽  
Author(s):  
Jia-Xing Yue ◽  
Jing Li ◽  
Louise Aigrain ◽  
Johan Hallin ◽  
Karl Persson ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Accumulation Rate ◽  
Population Level ◽  
Structural Rearrangements ◽  
Chromosome Partitioning ◽  
Long Read ◽  
Definition Of ◽  
Genome Assemblies ◽  
Reference Genomes

AbstractStructural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their evolutionary dynamics are difficult to characterize with short-read sequencing. Here, we report long-read sequencing for 12 strains representing major subpopulations of the partially domesticated yeastSaccharomyces cerevisiaeand its wild relativeSaccharomyces paradoxus. Complete genome assemblies and annotations generate population-level reference genomes and allow for the first explicit definition of chromosome partitioning into cores, subtelomeres and chromosome-ends. High-resolution view of structural dynamics uncovers that, in chromosomal cores,S. paradoxusexhibits higher accumulation rate of balanced structural rearrangements (inversions, translocations and transpositions) whereasS. cerevisiaeaccumulates unbalanced rearrangements (large insertions, deletions and duplications) more rapidly. In subtelomeres, recurrent interchromosomal reshuffling was found in both species, with higher rate inS. cerevisiae. Such striking contrasts between wild and domesticated yeasts reveal the influence of human activities on structural genome evolution.

scholarly journals RITAN: rapid integration of term annotation and network resources

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6994 ◽  
Author(s):  
Michael T. Zimmermann ◽  
Brian Kabat ◽  
Diane E. Grill ◽  
Richard B. Kennedy ◽  
Gregory A. Poland
Keyword(s):  
High Throughput ◽  
Network Biology ◽  
R Package ◽  
Network Resources ◽  
Function Annotation ◽  
Functional Annotations ◽  
Core Set ◽  
Term Enrichment ◽  
Multiple Network ◽  
High Throughput Experiments

Background Identifying the biologic functions of groups of genes identified in high-throughput studies currently requires considerable time and/or bioinformatics experience. This is due in part to each resource housed within separate databases, requiring users to know about them, and integrate across them. Time consuming and often repeated for each study, integrating across resources and merging with data under study is an increasingly common bioinformatics task. Methods We developed an open-source R software package for assisting researchers in annotating their genesets with functions, pathways, and their interconnectivity across a diversity of network resources. Results We present rapid integration of term annotation and network resources (RITAN) for the rapid and comprehensive annotation of a list of genes using functional term and pathway resources and their relationships among each other using multiple network biology resources. Currently, and to comply with data redistribution policies, RITAN allows rapid access to 16 term annotations spanning gene ontology, biologic pathways, and immunologic modules, and nine network biology resources, with support for user-supplied resources; we provide recommendations for additional resources and scripts to facilitate their addition to RITAN. Having the resources together in the same system allows users to derive novel combinations. RITAN has a growing set of tools to explore the relationships within resources themselves. These tools allow users to merge resources together such that the merged annotations have a minimal overlap with one another. Because we index both function annotation and network interactions, the combination allows users to expand small groups of genes using links from biologic networks—either by adding all neighboring genes or by identifying genes that efficiently connect among input genes—followed by term enrichment to identify functions. That is, users can start from a core set of genes, identify interacting genes from biologic networks, and then identify the functions to which the expanded list of genes contribute. Conclusion We believe RITAN fills the important niche of bridging the results of high-throughput experiments with the ever-growing corpus of functional annotations and network biology resources. Availability Rapid integration of term annotation and network resources is available as an R package at github.com/MTZimmer/RITAN and BioConductor.org.

scholarly journals DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shengjun Tan ◽  
Huijing Ma ◽  
Jinbo Wang ◽  
Man Wang ◽  
Mengxia Wang ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Replication Fork ◽  
Single Copy ◽  
Terminal Inverted Repeat ◽  
Gap Filling ◽  
New Genes ◽  
Repeat Dna ◽  
New Gene ◽  
Gene Structures ◽  
Reference Genomes

AbstractDespite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find that Ssk-FB4s represent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.

scholarly journals Unification of functional annotation descriptions using text mining

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pedro Queirós ◽  
Polina Novikova ◽  
Paul Wilmes ◽  
Patrick May
Keyword(s):  
Text Mining ◽  
Protein Function ◽  
Functional Annotation ◽  
Reference Data ◽  
Function Annotation ◽  
Functional Annotations ◽  
Data Source ◽  
Multiple References

Abstract A common approach to genome annotation involves the use of homology-based tools for the prediction of the functional role of proteins. The quality of functional annotations is dependent on the reference data used, as such, choosing the appropriate sources is crucial. Unfortunately, no single reference data source can be universally considered the gold standard, thus using multiple references could potentially increase annotation quality and coverage. However, this comes with challenges, particularly due to the introduction of redundant and exclusive annotations. Through text mining it is possible to identify highly similar functional descriptions, thus strengthening the confidence of the final protein functional annotation and providing a redundancy-free output. Here we present UniFunc, a text mining approach that is able to detect similar functional descriptions with high precision. UniFunc was built as a small module and can be independently used or integrated into protein function annotation pipelines. By removing the need to individually analyse and compare annotation results, UniFunc streamlines the complementary use of multiple reference datasets.

scholarly journals Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression

2021 ◽  
Author(s):  
Zhen Yue ◽  
Rongxue Ma ◽  
Denghu Cheng ◽  
Xing Yan ◽  
Yaping He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Genomic Structure ◽  
Ion Binding ◽  
Recombination Suppression ◽  
Stripe Pattern ◽  
Target Region ◽  
Gene Structures ◽  
Reference Genomes ◽  
Insight Into

Abstract Stripe pattern is an important commodity trait in watermelon, displaying diverse types. In this study, two segregating populations were generated for genetic mapping the single dominant locus ClSP, which was finally delimited to a 611.78 Kb interval with suppression of recombination. According to polymorphism sites detected among genotypes, four discrete haploblocks were characterized in this target region. Based on reference genomes, 81 predicted genes were annotated in the ClSP interval, including seven transcription factors namely as candidate No1-No7. Meanwhile, the ortholog gene of cucumber ist responsible for the irregular stripes was considered as candidate No8. Strikingly, gene structures of No1-No5 completely varied from their reference descriptions and subsequently re-annotated. Notably, the adjacent distribution candidates No2 and No3, as well as No4 and No5, were confirmed to derive from longer transcripts designated as No2_3 and No4_5, respectively. Sequence analysis demonstrated the third polymorphism in CDS of re-annotated No4_5 resulting in truncated proteins in non-stripe plants. Furthermore, only No4_5 was down-regulated in non-stripes relative to stripes contrast to other candidates. Transcriptome analysis identified 356 DEGs between striped and non-striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in non-stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in non-stripes, such as ERFs and WRKYs. This study not only contributes to a better understanding of the molecular mechanisms underlying watermelon stripe development, but also provides new insight into the genomic structure of ClSP locus and valuable candidates.

scholarly journals Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection

2018 ◽  
Author(s):  
M. Saitou ◽  
O. Gokcumen
Keyword(s):  
Phenotypic Diversity ◽  
Human Populations ◽  
Related Gene ◽  
Partial Duplication ◽  
Future Studies ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Insertion Sites ◽  
Reference Genomes

ABSTRACTPolymorphic duplications in humans have been shown to contribute to phenotypic diversity. However, the evolutionary forces that maintain variable duplications across the human genome are largely unexplored. To understand the haplotypic architecture of the derived duplications, we developed a linkage-disequilibrium based method to detect insertion sites of polymorphic duplications not represented in reference genomes. This method also allows resolution of haplotypes harboring the duplications. Using this approach, we conducted genome-wide analyses and identified the insertion sites of 22 common polymorphic duplications. We found that the majority of these duplications are intrachromosomal and only one of them is an interchromosomal insertion. Further characterization of these duplications revealed significant associations to blood and skin phenotypes. Based on population genetics analyses, we found that the partial duplication of a well-characterized pigmentation-related gene, HERC2, may be selected against in European populations. We further demonstrated that the haplotype harboring the partial duplication significantly affects the expression of the HERC2P9 gene in multiple tissues. Our study sheds light onto the evolutionary impact of understudied polymorphic duplications in human populations and presents methodological insights for future studies.

scholarly journals Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database

2016 ◽  
Vol 48 (8) ◽  
pp. 589-600 ◽  
Author(s):  
Shur-Jen Wang ◽  
Stanley J. F. Laulederkind ◽  
G. Thomas Hayman ◽  
Victoria Petri ◽  
Jennifer R. Smith ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Complex Disease ◽  
Biological Data ◽  
Disease Genes ◽  
Genome Database ◽  
Functional Annotations ◽  
Pathway Data ◽  
Genetic And Environmental Factors ◽  
Rat Genome

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.

scholarly journals Systematic Investigations of the ZF-HD Gene Family in Tobacco Reveal Their Multiple Roles in Abiotic Stresses

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 406
Author(s):  
Jinhao Sun ◽  
Minmin Xie ◽  
Xiaoxu Li ◽  
Zhiyuan Li ◽  
Qi Wang ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Gene Silencing ◽  
Abiotic Stresses ◽  
Multiple Roles ◽  
Virus Induced Gene Silencing ◽  
Nicotiana Tabacum L ◽  
Localization Analysis ◽  
Gene Structures ◽  
Functional Analyses ◽  
Profiling Analysis

Zinc finger homeodomain (ZF-HD) transcription factors play significant roles in plant growth and responses to environmental stresses. In this study, 32 ZF-HD genes identified in the tobacco (Nicotiana tabacum L.) genome were divided into six groups according to phylogenetic analysis with Arabidopsis and tomato ZF-HD members. An examination of gene structures and conserved motifs revealed the relatively conserved exon/intron structures and motif organization within each subgroup. In addition, various stress-related elements are found in the promoter region of these genes. The expression profiling analysis revealed that NtZF-HD genes expressed in different tissues and could be induced by several abiotic stresses. Notably, NtZF-HD21 was highly expressed in response to the drought treatments. Subcellular localization analysis and a virus-induced gene silencing (VIGS) experiment were performed to investigate the potential functions of NtZF-HD21. The subcellular localization indicated that NtZF-HD21 is a nuclear protein. Furthermore, gene silencing of the NtZF-HD21 gene reduced the drought resistance of tobacco. These findings provide insights for further biological functional analyses of the NtZF-HD genes in tobacco.

Microscopy of porous ceramics

1989 ◽  
Vol 47 ◽  
pp. 438-439
Author(s):  
H. M. Kerch ◽  
R. A. Gerhardt
Keyword(s):  
Porous Ceramics ◽  
Specimen Preparation ◽  
High Porosity ◽  
Ion Milling ◽  
Forming Process ◽  
Preparation Methods ◽  
Pore Texture ◽  
Proper Design ◽  
And Function ◽  
Function Information

Highly porous ceramics are employed in a variety of engineering applications due to their unique mechanical, optical, and electrical characteristics. In order to achieve proper design and function, information about the pore structure must be obtained. Parameters of importance include pore size, pore volume, and size distribution, as well as pore texture and geometry. A quantitative determination of these features for high porosity materials by a microscopic technique is usually not done because artifacts introduced by either the sample preparation method or the image forming process of the microscope make interpretation difficult.Scanning electron microscopy for both fractured and polished surfaces has been utilized extensively for examining pore structures. However, there is uncertainty in distinguishing between topography and pores for the fractured specimen and sample pullout obscures the true morphology for samples that are polished. In addition, very small pores (nm range) cannot be resolved in the S.E.M. On the other hand, T.E.M. has better resolution but the specimen preparation methods involved such as powder dispersion, ion milling, and chemical etching may incur problems ranging from preferential widening of pores to partial or complete destruction of the pore network.

Trial-based functional analyses as basis for elopement intervention.

2017 ◽  
Vol 17 (2) ◽  
pp. 166-173 ◽  
Author(s):  
Joseph M. Lambert ◽  
Crystal I. Finley ◽  
Carmen E. Caruthers
Keyword(s):  
Functional Analyses
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