scholarly journals A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2298
Author(s):  
Manosh Kumar Biswas ◽  
Dhima Biswas ◽  
Mita Bagchi ◽  
Ganjun Yi ◽  
Guiming Deng
Keyword(s):  
Draft Genome ◽  
Genome Survey ◽  
Plant Mirna ◽  
Wide Range ◽  
Intergenic Regions ◽  
Mirna Evolution ◽  
Taxonomic Groups ◽  
Genome Assemblies ◽  
User Friendly ◽  
Simple Sequence

Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.

scholarly journals SorghumBase: a web-based portal for sorghum genetic information and community advancement

Planta ◽  
2022 ◽  
Vol 255 (2) ◽  
Author(s):  
Nicholas Gladman ◽  
Andrew Olson ◽  
Sharon Wei ◽  
Kapeel Chougule ◽  
Zhenyuan Lu ◽  
...  
Keyword(s):  
Resource Sharing ◽  
Content Management ◽  
Research Community ◽  
Data Types ◽  
Training Materials ◽  
Wide Range ◽  
Variant Information ◽  
Data Collation ◽  
Genome Assemblies ◽  
User Friendly

Abstract Main conclusion SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal (https://www.sorghumbase.org), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.

scholarly journals FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies

2021 ◽  
Vol 15 ◽  
pp. 117793222110592
Author(s):  
Enzo Guerrero-Araya ◽  
Marina Muñoz ◽  
César Rodríguez ◽  
Daniel Paredes-Sabja
Keyword(s):  
Multilocus Sequence Typing ◽  
Draft Genome ◽  
Housekeeping Genes ◽  
Divide And Conquer ◽  
Speed Test ◽  
Processing Times ◽  
Large Numbers ◽  
Wide Range ◽  
Public Repositories ◽  
Genome Assemblies

Multilocus Sequence Typing (MLST) is a precise microbial typing approach at the intra-species level for epidemiologic and evolutionary purposes. It operates by assigning a sequence type (ST) identifier to each specimen, based on a combination of alleles of multiple housekeeping genes included in a defined scheme. The use of MLST has multiplied due to the availability of large numbers of genomic sequences and epidemiologic data in public repositories. However, data processing speed has become problematic due to the massive size of modern datasets. Here, we present FastMLST, a tool that is designed to perform PubMLST searches using BLASTn and a divide-and-conquer approach that processes each genome assembly in parallel. The output offered by FastMLST includes a table with the ST, allelic profile, and clonal complex or clade (when available), detected for a query, as well as a multi-FASTA file or a series of FASTA files with the concatenated or single allele sequences detected, respectively. FastMLST was validated with 91 different species, with a wide range of guanine-cytosine content (%GC), genome sizes, and fragmentation levels, and a speed test was performed on 3 datasets with varying genome sizes. Compared with other tools such as mlst, CGE/MLST, MLSTar, and PubMLST, FastMLST takes advantage of multiple processors to simultaneously type up to 28 000 genomes in less than 10 minutes, reducing processing times by at least 3-fold with 100% concordance to PubMLST, if contaminated genomes are excluded from the analysis. The source code, installation instructions, and documentation of FastMLST are available at https://github.com/EnzoAndree/FastMLST

scholarly journals The draft genome sequence of the grove snail Cepaea nemoralis

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Suzanne V Saenko ◽  
Dick S J Groenenberg ◽  
Angus Davison ◽  
Menno Schilthuizen
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Agricultural Pests ◽  
Shell Color ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Edible Species ◽  
Wide Range ◽  
In Captivity ◽  
Long Read

Abstract Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of “supergenes,” as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.

The Intelligent Design of the Gear Reducer

2012 ◽  
Vol 522 ◽  
pp. 823-827
Author(s):  
Jian Jiang Fang ◽  
Wen Jun Qi
Keyword(s):  
Intelligent Design ◽  
Object Oriented ◽  
Data Access ◽  
Mechanical Transmission ◽  
Design Efficiency ◽  
Integrated Technology ◽  
Gear Drive ◽  
Object Oriented Technology ◽  
Wide Range ◽  
User Friendly

The gear drive is the wide range of applications and is particularly important as a form of mechanical transmission, but the design process requires large amounts of data access and computation. In the paper, computer integrated technology and object-oriented technology is used to research and develop the intelligent design of Straight gear reducer system with user-friendly interactive platform, easy to use, high design efficiency and reliable data.

scholarly journals Relationships among cultivated peas and their wild relatives: Molecular and morphological characterization

2019 ◽  
Vol 48 (4) ◽  
pp. 1011-1019
Author(s):  
Fatih Hanci ◽  
Esra Cebeci
Keyword(s):  
Molecular Study ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Local Varieties ◽  
Ssr Loci ◽  
Taxonomic Groups ◽  
Clustering Pattern ◽  
Polymorphism Level ◽  
Different Sources ◽  
Simple Sequence

This study was conducted to determine relationship between some wild pea accessions (Pisum fulvum L., P. abyssinicum L., P. sativum var. elatius), local varieties (P. sativum var. sativum L. and P. sativum var. arvense L.) and commercial varieties “Boogie” and “Rondo”. The genetic diversity was evaluated with 14 simple sequence repeat markers and 50 morphological characters. The results of morphology indicated that, genotypes showed a clustering pattern based on the taxonomic groups when considering only flower characters and all morphological characters. During the molecular study, a total of 48 alleles were obtained. Used all primers showed polymorphism in accessions. The number of alleles varied between 2 - 6 among 14 SSR loci revealing the polymorphism level of markers. Similarity coefficient (Dice’s) ranged from 0.100 to 0.800 with an average of 0.378. A dendrogram grouped the 15 genotypes into two main clusters. This information can be utilized for genetic analysis, genotype identification from different sources and development of improved germplasm.

The Dose Determines the Stimulation (and Poison): Development of A Chemical Hormesis Database

1997 ◽  
Vol 16 (6) ◽  
pp. 545-559 ◽  
Author(s):  
Edward J. Calabrese ◽  
Linda A. Baldwin
Keyword(s):  
A Priori ◽  
Dose Range ◽  
Evaluation Criteria ◽  
Metabolic Effects ◽  
Growth Responses ◽  
Wide Range ◽  
Order Of Magnitude ◽  
Real Phenomenon ◽  
Effect Level ◽  
Taxonomic Groups

A comprehensive effort was undertaken to identify articles demonstrating chemical hormesis. Nearly 4000 potentially relevant articles were retrieved from preliminary computer searches utilizing various keyword descriptors and extensive cross-referencing. A priori evaluation criteria were established including study design features (e.g., number of doses, dose range), statistical analysis, and reproducibility of results. Evidence of chemical hormesis was judged to have occurred in approximately 350 of the 4000 studies evaluated. Chemical hormesis was observed in a wide range of taxonomic groups and involved agents representing highly diverse chemical classes, many of potential environmental relevance. Numerous biologic endpoints were assessed, with growth responses the most prevalent, followed by metabolic effects, longevity, reproductive responses, and survival. Hormetic responses were generally observed to be of limited magnitude with the average low-dose maximum stimulation approximately 50% greater than controls. The hormetic dose-response range was generally limited to about one order of magnitude with the upper end of the hormetic curve approaching the estimated no-observed-effect level (NOEL) for the particular endpoint. Based on the evaluation criteria, high to moderate evidence of hormesis was observed in studies comprised of ≥ doses with <3 doses in the hormetic zone. The present analysis suggests that chem ical hormesis is a reproducible and generalizable biologic phenomenon. Over the last decade advances have been made providing mechanistic insight helpful in explaining the phenomenon of chemical hormesis in multiple biologic systems with various endpoints. The reason for the uncertainty surrounding the existence of hormesis as a “real phenomenon” is believed to be the result of its relatively infrequent observation in the literature due to experimental design considerations, especially with respect to the number of doses, range of doses, and endpoint selection.

Users’ Attitudes towards Institutional Repository in Jadavpur University: A Critical Study

2012 ◽  
Vol 1 (2) ◽  
pp. 45-52
Author(s):  
Sambhu Nath Halder ◽  
Suvra Chandra
Keyword(s):  
Potential Role ◽  
Point Of View ◽  
Academic Institution ◽  
Critical Study ◽  
Institutional Repository ◽  
Digital Environment ◽  
Institutional Repositories ◽  
Wide Range ◽  
User Friendly

This paper examines the user-aware of institutional repositories in Jadavpur University. The main objective of this study is to investigate the awareness of Institutional Repository (IR) in an academic institution and different aspects associated with it, such as, software, sources for user’s awareness, motivators for developing a repository, demand of the users in changing paradigms from traditional to digital environment, etc. In the present days, libraries are also adopting the latest technologies to provide best possible services in user friendly form. This paper also describes the potential role of institutional repositories and its easiness and simplicity of use are attracting more patrons in the use of institutional repositories. Only a wide range of user awareness is needed for proper usage of its beauty. Entirely this paper is based on a critical study, which measures the utility of institutional repositories in users’ point of view.

Bring Out Your Data

2012 ◽  
pp. 126-145
Author(s):  
Thomas E. Grissom ◽  
Andrew DuKatz ◽  
Hubert A. Kordylewski ◽  
Richard P. Dutton
Keyword(s):  
Cost Effective ◽  
Regulatory Oversight ◽  
Measurement Quality ◽  
Related Data ◽  
Healthcare Data ◽  
Effective Manner ◽  
Wide Range ◽  
Automated Process ◽  
User Friendly ◽  
Quality Institute

Recent healthcare legislation, financial pressures, and regulatory oversight have increased the need to create improved mechanisms for performance measurement, quality management tracking, and outcomes-based research. The Anesthesia Quality Institute (AQI) has established the National Anesthesia Clinical Outcomes Registry (NACOR) to support these requirements for a wide-range of customers including individual anesthesiologists, anesthesia practices, hospitals, and credentialing agencies. Concurrently, the availability of increased digital sources of healthcare data make it possible to capture massive quantities of data in a more efficient and cost-effective manner than ever before. With NACOR, AQI has established a user-friendly, automated process to effectively and efficiently collect a wide-range of anesthesia-related data directly from anesthesia practices. This review will examine the issues guiding the evolution of NACOR as well as some potential pitfalls in its growth and usage.

Social Networks and Internet Communities in the Field of Geographic Information and Their Role in Open Data Government Initiatives

2015 ◽  
pp. 1586-1618
Author(s):  
Paula Díaz ◽  
Joan Masó
Keyword(s):  
Open Data ◽  
User Generated Content ◽  
Geospatial Information ◽  
Global Networks ◽  
New Era ◽  
Traditional Procedure ◽  
Wide Range ◽  
Relevant Role ◽  
Feasible Alternative ◽  
User Friendly

Users are playing an increasingly relevant role in geospatial data production. The traditional procedure for creating cartography, mainly by experts in official mapping agencies, has evolved into a more participative process for generating data: neogeography. Technology and the Internet are now user-friendly for a wide range of people who have become active users of global networks, such as GEOSS, INSPIRE, Eye On Earth, and EarthCube, and official producers need to adapt to the new era of openness, collaboration, and hybrid maps by adopting open standards. Although the creation of geospatial information is notably growing worldwide, and is enhanced by user-generated content, we may wonder whether this is a feasible alternative to official cartography. This chapter reviews the main geospatial networks based on both bottom-up and top-down data creation approaches, as well as the potentialities and limitations of user-generated content in the scientific field and in decision-making organisms.

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