TAXONOMIC ASSIGNMENT OF TWO EOCENE ENTELODONT MANDIBLES FROM THE OGLALA NATIONAL GRASSLANDS

2018 ◽  
Author(s):  
Kristen Hirst ◽  
◽  
D.R. Schmidt ◽  
Chris Mooney
Keyword(s):  
Taxonomic Assignment

scholarly journals Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Congyu Lu ◽  
Zheng Zhang ◽  
Zena Cai ◽  
Zhaozhong Zhu ◽  
Ye Qiu ◽  
...  
Keyword(s):  
Prediction Accuracy ◽  
Functional Characterization ◽  
Gaussian Model ◽  
Software Tool ◽  
Biological Properties ◽  
Rapid Identification ◽  
Taxonomic Assignment ◽  
Genus Level ◽  
Alignment Free ◽  
Archaeal Viruses

Abstract Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.

scholarly journals EpicPCR 2.0: Technical and Methodological Improvement of a Cutting-Edge Single-Cell Genomic Approach

2021 ◽  
Vol 9 (8) ◽  
pp. 1649
Author(s):  
Véronica L. Roman ◽  
Christophe Merlin ◽  
Marko P. J. Virta ◽  
Xavier Bellanger
Keyword(s):  
Microbial Communities ◽  
Single Cell ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Environmental Matrices ◽  
Taxonomic Assignment ◽  
Integrative And Conjugative Elements ◽  
Functional Sequence ◽  
Methodological Improvement ◽  
New Gene

EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.

Revisiting the type of Cespitularia stolonifera Gohar, 1938 leads to the description of a new genus and a species of the family Xeniidae (Octocorallia, Alcyonacea)

Zootaxa ◽  
2021 ◽  
Vol 4964 (2) ◽  
pp. 330-344
Author(s):  
YEHUDA BENAYAHU ◽  
LEEN P. VAN OFWEGEN ◽  
J. P. RUIZ ALLAIS ◽  
CATHERINE S. MCFADDEN
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Soft Coral ◽  
Taxonomic Assignment ◽  
Coral Genus ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Membranous Part ◽  
Green Island ◽  
A New Species

Because of the problematical identity and status of the type of the xeniid soft coral genus Cespitularia Milne-Edwards & Haime, 1850, the species C. stolonifera Gohar, 1938 is revised. Examination of the type colonies has led to the establishment of the new genus Unomia gen. n. which is described and depicted. This genus features a stalk, commonly divided into branches featuring a diffuse polypiferous part consisting of distal clustered polyps and proximal individual ones on the stalk or the basal membranous part of the colonies. The sclerites are ellipsoid platelets composed of dendritic calcite rods whose tips are distinct on the surface of the platelets. Freshly collected material from Venezuelan reefs where the species is invasive was subjected to molecular phylogenetic analysis, the results of which substantiate the taxonomic assignment of the new genus under U. stolonifera comb. n. A new species, U. complanatis, from Japan and Green Island (Taiwan) is described and further illustrates the extent of the interspecific morphological variation within the genus. The results reveal that the biogeographic distribution of Unomia gen. n. includes Pacific Ocean reefs in addition to the previously reported invaded Caribbean reefs. 

scholarly journals Taxonomic assignment for large-scale metagenomic data on high-perfomance systems

2017 ◽  
Vol 33 (2) ◽  
pp. 119-130
Author(s):  
Vinh Van Le ◽  
Hoai Van Tran ◽  
Hieu Ngoc Duong ◽  
Giang Xuan Bui ◽  
Lang Van Tran
Keyword(s):  
High Performance Computing ◽  
Assignment Problem ◽  
High Performance ◽  
Large Scale ◽  
Computing System ◽  
Metagenomic Data ◽  
Taxonomic Assignment ◽  
High Performance Computing System ◽  
Powerful Approach ◽  
Performance Computing

Metagenomics is a powerful approach to study environment samples which do not require the isolation and cultivation of individual organisms. One of the essential tasks in a metagenomic project is to identify the origin of reads, referred to as taxonomic assignment. Due to the fact that each metagenomic project has to analyze large-scale datasets, the metatenomic assignment is very much computation intensive. This study proposes a parallel algorithm for the taxonomic assignment problem, called SeMetaPL, which aims to deal with the computational challenge. The proposed algorithm is evaluated with both simulated and real datasets on a high performance computing system. Experimental results demonstrate that the algorithm is able to achieve good performance and utilize resources of the system efficiently. The software implementing the algorithm and all test datasets can be downloaded at http://it.hcmute.edu.vn/bioinfo/metapro/SeMetaPL.html.

scholarly journals In situ filamentous communities from the Ediacaran (approx. 563 Ma) of Brazil

2021 ◽  
Vol 288 (1942) ◽  
pp. 20202618
Author(s):  
Bruno Becker-Kerber ◽  
Gabriel Eduardo Baréa de Barros ◽  
Paulo Sergio Gomes Paim ◽  
Gustavo M. E. M. Prado ◽  
Ana Lucia Zucatti da Rosa ◽  
...  
Keyword(s):  
Oxygen Concentration ◽  
Benthic Communities ◽  
Preferred Orientation ◽  
Redox Condition ◽  
Taxonomic Assignment ◽  
Diagnostic Features ◽  
Ecological Dynamics ◽  
Widespread Occurrence ◽  
Biological Affinity

Precambrian filamentous microfossils are common and diverse. Nevertheless, their taxonomic assignment can be difficult owing to their overall simple shapes typically lacking in diagnostic features. Here, we report in situ communities of well-preserved, large filamentous impressions from the Ediacaran Itajaí Basin ( ca 563 Ma) of Brazil. The filaments are uniserial (unbranched) and can reach up to 200 µm in width and up to 44 mm in length. They occur as both densely packed or sparsely populated surfaces, and typically show a consistent orientation. Although simple in shape, their preferred orientation suggests they were tethered to the seafloor, and their overall flexibility (e.g. bent, folded and twisted) supports a biological (rather than sedimentary) affinity. Biometric comparisons with modern filamentous groups further support their biological affinity, suggesting links with either large sulfide-oxidizing bacteria (SOB) or eukaryotes. Other morphological and palaeoecological characteristics further corroborates their similarities with modern large filamentous SOB. Their widespread occurrence and association with complex Ediacaran macrobiota (e.g. frondose organisms, Palaeopascichnus ) suggest that they probably played an important role in the ecological dynamics of these early benthic communities by providing firm substrates for metazoans to inhabit. It is further hypothesized that the dynamic redox condition in the latest Ediacaran, with the non-continuous rise in oxygen concentration and periods of hypoxia, may have created ideal conditions for SOB to thrive.

The Earliest South African Hominids

2021 ◽  
Vol 50 (1) ◽  
pp. 125-143
Author(s):  
Ronald J. Clarke ◽  
Travis Rayne Pickering ◽  
Jason L. Heaton ◽  
Kathleen Kuman
Keyword(s):  
East Africa ◽  
South African ◽  
The South ◽  
Taxonomic Assignment ◽  
First Time ◽  
Over Time

The earliest South African hominids (humans and their ancestral kin) belong to the genera Australopithecus, Paranthropus, and Homo, with the oldest being a ca. 3.67 million-year-old nearly complete skeleton of Australopithecus (StW 573) from Sterkfontein Caves. This skeleton has provided, for the first time in almost a century of research, the full anatomy of an Australopithecus individual with indisputably associated skull and postcranial bones that give complete limb lengths. The three genera are also found in East Africa, but scholars have disagreed on the taxonomic assignment for some fossils owing to historical preconceptions. Here we focus on the South African representatives to help clarify these debates. The uncovering of the StW 573 skeleton in situ revealed significant clues concerning events that had affected it over time and demonstrated that the associated stalagmite flowstones cannot provide direct dating of the fossil, as they are infillings of voids caused by postdepositional collapse.

scholarly journals Variations in genetic structure and male genitalia suggest recent lineage diversification in the Neotropical dung beetle complex Canthon cyanellus (Scarabaeidae: Scarabaeinae)

2020 ◽  
Vol 131 (3) ◽  
pp. 505-520
Author(s):  
Janet Nolasco-Soto ◽  
Mario E Favila ◽  
Alejandro Espinosa De Los Monteros ◽  
Jorge González-Astorga ◽  
Gonzalo Halffter ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Morphological Variation ◽  
Male Genitalia ◽  
Morphological Variability ◽  
Dung Beetle ◽  
Morphological Characters ◽  
Taxonomic Assignment ◽  
Morphometric Variation ◽  
Evolutionary Forces ◽  
Significant Genetic Structure

Abstract We analysed the genetic divergence and morphology of the aedeagus (i.e. phallobase and parameres) in Canthon cyanellus at different geographical levels. The results from both approaches were compared with the current taxonomic assignment of the C. cyanellus complex, which includes three subspecies. We found a high variation in all the morphological characters of the aedeagus in the populations analysed; the morphometric variation was not geographically structured, either by population or by region. The genealogical analysis indicates a significant genetic structure that does not match either the morphological variation in the male genitalia or the previous subspecific taxonomic classification. Our results suggest that the morphological variation of the aedeagus is seemingly not an isolating reproductive barrier and that the intra- and interpopulation morphological variability of the aedeagus in the C. cyanellus complex does not permit the division into several species. We suggest that other evolutionary forces, such as genetic drift and sexual selection, have influenced the evolution of the male genitalia and the incipient differentiation of this species complex.

scholarly journals Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

2019 ◽  
Vol 37 (6) ◽  
pp. 632-639 ◽  
Author(s):  
Ho Bin Jang ◽  
Benjamin Bolduc ◽  
Olivier Zablocki ◽  
Jens H. Kuhn ◽  
Simon Roux ◽  
...  
Keyword(s):  
Taxonomic Assignment ◽  
Virus Genomes ◽  
Gene Sharing

scholarly journals Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marius Welzel ◽  
Anja Lange ◽  
Dominik Heider ◽  
Michael Schwarz ◽  
Bernd Freisleben ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Workflow Management ◽  
Amplicon Sequencing ◽  
Version Control ◽  
Marker Genes ◽  
Sequencing Data ◽  
Taxonomic Assignment ◽  
Ecological Processes ◽  
Link Type ◽  
User Friendly

Abstract Background Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system. Results We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix). Conclusion Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.

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