scholarly journals Microbial Genomic Taxonomy.

2021 ◽  
pp. 168-178
Author(s):  
Cristiane C. Thompson ◽  
Livia Vidal ◽  
Vinicius Salazar ◽  
Jean Swings ◽  
Fabiano L. Thompson
Keyword(s):  
Open Access ◽  
Genome Sequences ◽  
Culture Collections ◽  
Taxonomic Descriptions ◽  
Novel Approach ◽  
Online Databases ◽  
Genomic Taxonomy ◽  
Microbial Taxonomy ◽  
Novel Taxa ◽  
Alternative Code

Abstract This book chapter argues for an open-access catalogue of taxonomic descriptions with prototypes; diagnostic tables; and links to culture collections, to genome and gene sequences, and to other phenotypic and ecological databases. Ideally, the open access taxonomy will be based solely on genome sequences that allow both the phylogenetic allocation of new strains and species in the taxonomic space and the phenotypic/metabolic characterization in open online databases. Careful and thorough annotation of the genome sequences for function and chemotaxonomic data will be required. An alternative Code will be required for the naming strategy of genomes. Current microbial taxonomy is not able to keep up with the pace of development in microbial ecology. Innovative ways of developing microbial taxonomy are, therefore, needed urgently. This novel approach can, for the first time, allow microbial species descriptions using genomes based on ecological and evolutionary theory. One challenge ahead is to leverage the use of genome sequences to obtain insights on the (in silico) phenotypes and ecology of novel taxa.

Myrcia (Myrtaceae) in the state of Paraná, Brazil

Phytotaxa ◽  
2021 ◽  
Vol 486 (1) ◽  
pp. 1-105
Author(s):  
LAURA C. DE LANNOY ◽  
AYRTON I. DE OLIVEIRA ◽  
RENATO GOLDENBERG ◽  
DUANE F. LIMA
Keyword(s):  
South America ◽  
Central America ◽  
Herbarium Specimens ◽  
Vegetation Types ◽  
Northern Limit ◽  
Southern South America ◽  
Taxonomic Descriptions ◽  
Online Databases ◽  
The Caribbean ◽  
Doubtful Species

Myrtaceae is one of the largest families in number of species within the order Myrtales and one of the richest families in Brazil. Myrcia is the fourth largest genus of Myrtaceae, with approximately 770 species distributed from Central America and the Caribbean to southern South America. In Brazil Myrcia is represented by 397 species, of which 309 are endemic. In this study, we present the taxonomic treatment for all species of Myrcia that occur in Paraná state, Brazil. Analyses of herbarium specimens, online databases, and bibliography were performed. Fifty-three species of Myrcia occur in Paraná, distributed in all vegetation types. Twenty-three names were excluded from previous lists of species or listed as doubtful species. Neither of the recorded species is endemic to Paraná, but this state is the southern and northern limit of distribution of six and two species, respectively. We present an identification key, taxonomic descriptions, figures, maps, and comments on phenology, habitat, and morphology for each species.

scholarly journals Analyzing University of Virginia Health publications using open data, Python, and Streamlit

2021 ◽  
Vol 109 (4) ◽  
Author(s):  
Anson Parker ◽  
Abbey Heflin ◽  
Lucy Carr Jones
Keyword(s):  
Open Access ◽  
Data Visualization ◽  
Web Of Science ◽  
Open Data ◽  
Health Sciences ◽  
Open Access Publishing ◽  
University Of Virginia ◽  
Data Set ◽  
Novel Approach ◽  
Rest Api

As part of a larger project to understand the publishing choices of UVA Health authors and support open access publishing, a team from the Claude Moore Health Sciences Library analyzed an open data set from Europe PMC, which includes metadata from PubMed records. We used the Europe PMC REST API to search for articles published in 2017–2020 with “University of Virginia” in the author affiliation field. Subsequently, we parsed the JSON metadata in Python and used Streamlit to create a data visualization from our public GitHub repository. At present, this shows the relative proportions of open access versus subscription-only articles published by UVA Health authors. Although subscription services like Web of Science, Scopus, and Dimensions allow users to do similar analyses, we believe this is a novel approach to doing this type of bibliometric research with open data and open source tools.  

scholarly journals Diat.barcode, an open-access curated barcode library for diatoms

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Frédéric Rimet ◽  
Evgenuy Gusev ◽  
Maria Kahlert ◽  
Martyn G. Kelly ◽  
Maxim Kulikovskiy ◽  
...  
Keyword(s):  
Open Access ◽  
Aquatic Ecosystems ◽  
High Throughput Sequencing ◽  
Lower Cost ◽  
Sequencing Data ◽  
Reference Library ◽  
Culture Collections ◽  
Nucleotide Database ◽  
Environmental Sequences ◽  
Level Identification

Abstract Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database.

scholarly journals Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
D Libkind ◽  
N Čadež ◽  
D A Opulente ◽  
Q K Langdon ◽  
C A Rosa ◽  
...  
Keyword(s):  
Sexual Behaviors ◽  
Yeast Species ◽  
Novel Species ◽  
Genetic Distances ◽  
Biological Research ◽  
Genome Sequences ◽  
Novel Taxa ◽  
Bioinformatic Approaches ◽  
Species Descriptions ◽  
Complete Genomic

ABSTRACT In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.

scholarly journals The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Okba Selama ◽  
Phillip James ◽  
Farida Nateche ◽  
Elizabeth M. H. Wellington ◽  
Hocine Hacène
Keyword(s):  
Geographical Area ◽  
Geographic Area ◽  
Global Scale ◽  
Service Access ◽  
Novel Approach ◽  
Online Databases ◽  
The Usa ◽  
Nucleotide Database ◽  
Bacterial Biodiversity

Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, whileE-utilitiesandPythonwere used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that theProteobacteriaare the most abundant and widely distributed phylum within both databases.

scholarly journals Forests’ First Decade: A Bibliometric Analysis Overview

Forests ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 72 ◽  
Author(s):  
Juan Uribe-Toril ◽  
José Ruiz-Real ◽  
Julia Haba-Osca ◽  
Jaime de Pablo Valenciano
Keyword(s):  
Open Access ◽  
Bibliometric Analysis ◽  
Forest Ecology ◽  
Scientific Information ◽  
Open Access Journal ◽  
Open Access Publishing ◽  
Online Databases ◽  
Graphical Visualization ◽  
Interdisciplinary Knowledge ◽  
Knowledge Area

Forests is a Swiss open access journal in the field of forestry and forest ecology founded in 2010. Currently, the journal celebrates its 10th anniversary. Therefore, the purpose of this research for the special issue A Decade of Forests Open Access Publishing is to present a whole bibliometric overview of the journal and highlight the state of the art of forestry as an interdisciplinary knowledge area. A bibliometric analysis of 2094 articles, reviews, editorials and corrections was conducted using two different scientific information platforms which publish indexes in online databases: Web of Science (WoS) and Scopus. The most influential countries and their relationship with funding institutions, the most leading and outstanding authors and the most significant articles published in Forests have been analyzed. A complete keyword concurrence network with a graphical visualization and a cluster analysis are adopted for identifying the main trends and opening issues to address in the coming decade, such as genetic diversity, forest productivity, resistance or resilience. This article has identified climate change, remote sensing, biomass and forest management as the main trends in forestry research during the last ten years.

scholarly journals High-Quality Draft Genome Sequences of Three Cyanobacteria Isolated from the Limestone Walls of the Old Cathedral of Coimbra, Portugal

2020 ◽  
Vol 9 (26) ◽  
Author(s):  
Fabiana Soares ◽  
João Trovão ◽  
Catarina Coelho ◽  
Inês Costa ◽  
Nuno Mesquita ◽  
...  
Keyword(s):  
Draft Genome ◽  
World Heritage Site ◽  
The Novel ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Heritage Site ◽  
Unesco World Heritage Site ◽  
Novel Taxa ◽  
High Quality Genome

ABSTRACT The recently described species Myxacorys almedinensis and two other cyanobacteria were isolated from the limestone walls of the Old Cathedral of Coimbra, Portugal (UNESCO World Heritage Site). The high-quality genome sequences presented here will be essential for characterization purposes and description of the novel taxa.

scholarly journals Novel Taxa Associated with Human Fungal Black-Grain Mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov.

2016 ◽  
Vol 54 (7) ◽  
pp. 1738-1745 ◽  
Author(s):  
Andrew M. Borman ◽  
Marie Desnos-Ollivier ◽  
Colin K. Campbell ◽  
Paul D. Bridge ◽  
Eric Dannaoui ◽  
...  
Keyword(s):  
Radical Surgery ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Culture Collections ◽  
Content Type ◽  
Azole Antifungals ◽  
Appropriate Treatment ◽  
Novel Taxa

Eumycetoma is a debilitating, chronic, fungal infection that is endemic in India, Indonesia, and parts of Africa and South and Central America. It remains a neglected tropical disease in need of international recognition. Infections follow traumatic implantation of saprophytic fungi and frequently require radical surgery or amputation in the absence of appropriate treatment. Several fungal species can cause black-grain mycetomas, includingMadurellaspp. (Sordariales),Falciformisporaspp.,Trematosphaeria grisea,Biatriospora mackinnonii,Pseudochaetosphaeronema larense, andMedicopsis romeroi(allPleosporales). We performed phylogenetic analyses based on five loci on 31 isolates from two international culture collections to establish the taxonomic affiliations of fungi that had been isolated from cases of black-grain mycetoma and historically classified asMadurella grisea. Although most strains were well resolved to species level and corresponded to known agents of eumycetoma, six independent isolates, which failed to produce conidia under any conditions tested, were only distantly related to existing members of thePleosporales. Five of the six isolates shared >99% identity with each other and are described asEmarellia griseagen. nov. and sp. nov; the sixth isolate represents a sister species in this novel genus and is described asEmarellia paragrisea.SeveralE. griseaisolates were present in both United Kingdom and French culture collections and had been isolated independently over 6 decades from cases of imported eumycetoma. Four of the six isolates involved patients that had originated on the Indian subcontinent. All isolates were all susceptiblein vitroto the azole antifungals, but had elevated MICs with caspofungin.

scholarly journals Complete Genome Sequences of Trifolium spp. Inoculant Strains Rhizobium leguminosarum sv. trifolii TA1 and CC275e: Resources for Genomic Study of the Rhizobium-Trifolium Symbiosis

2020 ◽  
pp. MPMI-08-20-0220
Author(s):  
Benjamin J. Perry ◽  
Shaun Ferguson ◽  
Aurelie Laugraud ◽  
Steve A. Wakelin ◽  
Wayne Reeve ◽  
...  
Keyword(s):  
New Zealand ◽  
Open Access ◽  
Complete Genome ◽  
Rhizobium Leguminosarum ◽  
Nitrogen Fixing ◽  
Genome Sequences ◽  
Future Studies ◽  
Genomic Study ◽  
Commercial Inoculant ◽  
Open Access Article

Rhizobium leguminosarum symbiovar trifolii strains TA1 and CC275e are nitrogen-fixing microsymbionts of Trifolium spp. and have been used as commercial inoculant strains for clovers in pastoral agriculture in Australia and New Zealand. Here we present the complete genome sequences of both strains, resolving their multipartite genome structures and allowing for future studies using genomic approaches. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

scholarly journals Tracking human population structure through time from whole genome sequences

2019 ◽  
Author(s):  
Ke Wang ◽  
Iain Mathieson ◽  
Jared O’Connell ◽  
Stephan Schiffels
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Demographic History ◽  
Time Dependent ◽  
Human Populations ◽  
Whole Genome ◽  
Genome Sequences ◽  
Migration Model ◽  
Novel Approach ◽  
Different Populations

AbstractThe genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population’s history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to analyse the population separation history. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago.Author SummaryHuman demographic history is reflected in specific patterns of shared mutations between the genomes from different populations. Here we aim to unravel this pattern to infer population structure through time with a new approach, called MSMC-IM. Based on estimates of coalescence rates within and across populations, MSMC-IM fits a time-dependent migration model to the pairwise rate of coalescences. We implemented this approach as an extension to existing software (MSMC2), and tested it with simulations exhibiting different histories of admixture and gene flow. We then applied it to the genomes from 15 worldwide populations to reveal their pairwise separation history ranging from a few thousand up to several million years ago. Among other results, we find evidence for remarkably deep population structure in some African population pairs, suggesting that deep ancestry dating to one million years ago and older is still present in human populations in small amounts today.

Sign in / Sign up

Export Citation Format

Share Document