scholarly journals What is an archaeon and are the Archaea really unique?

2018 ◽  
Author(s):  
Ajith Harish
Keyword(s):  
Sequence Data ◽  
Deep Structure ◽  
Distribution Patterns ◽  
Primary Sequence ◽  
Genomic Signatures ◽  
Multiple Datasets ◽  
Technical Advances ◽  
Small Set ◽  
Major Branch ◽  
Core Genes

AbstractThe recognition of the group Archaea as a major branch of the Tree of Life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. Here, to explore the causes for this persistent ambiguity, I examine multiple datasets that support contradicting conclusions. Results indicate that the uncertainty is primarily due to a scarcity of information in standard datasets — the core genes datasets — to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties, which supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limits of primary sequence data in resolving difficult phylogenetic problems and casts doubt on evolutionary inferences drawn solely from the analyses of a small set of core genes.

scholarly journals What is an archaeon and are the Archaea really unique?

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5770 ◽  
Author(s):  
Ajith Harish
Keyword(s):  
Sequence Data ◽  
Deep Structure ◽  
Distribution Patterns ◽  
Primary Sequence ◽  
Sequence Alignments ◽  
Evolutionary Transitions ◽  
Genomic Signatures ◽  
Substitution Mutations ◽  
Major Branch ◽  
Core Genes

The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets—universal core-genes datasets—to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.

scholarly journals A Preliminary Investigation of Marine Yeast Biodiversity in New Zealand Waters

2021 ◽  
Author(s):  
◽  
Melissa Francis
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Preliminary Investigation ◽  
Distribution Patterns ◽  
Marine Yeasts ◽  
Marine Yeast ◽  
Yeast Biomass ◽  
Ecological Implications ◽  
Terrestrial Environments ◽  
Biocontrol Potential

<p>This is the first known investigation of marine yeast biodiversity from waters surrounding New Zealand’s main Islands. Marine yeasts were cultured onto agar plates from algae sampled at three locations in the Wellington Region. DNA extractions and PCR amplifications of the internal transcribed spacer (ITS) regions were conducted, and resultant sequence data were used for isolate identification and phylogenetic analysis. Yeasts isolated during this investigation were not unique; seventy-four isolates were identified from a range of genera that are frequently detected in marine and terrestrial environments worldwide. Furthermore, high ITS sequence similarity was observed between yeasts isolated during this investigation and those from geographically distant locations. These findings may indicate that marine yeasts are ubiquitous at a global level, although evidence is insufficient as to whether yeasts also demonstrate biogeographic distribution patterns. Yeasts isolated during this investigation may have ecological implications in New Zealand’s marine environment; marine yeasts are likely to play a general saprophytic role and certain genera are pathogenic. Isolates were also identified from genera that have previously demonstrated beneficial properties and applications, including the production of useful compounds and highly nutritious yeast biomass, biocontrol potential against the postharvest decay of produce, and degradation abilities that may enable bioremediation of polluted marine environments.</p>

scholarly journals Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs

2019 ◽  
pp. 83-103
Author(s):  
Cristina Cruz ◽  
Jonathan Houseley
Keyword(s):  
Molecular Biology ◽  
Sequence Data ◽  
Noncoding Rnas ◽  
Northern Blotting ◽  
Northern Analysis ◽  
Standard Laboratory ◽  
Agarose Gels ◽  
The Past ◽  
Technical Advances ◽  
Biology Lab

AbstractOver the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights into ncRNA distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex RNA populations but are rarely employed outside specialist RNA research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated RNA on agarose gels and heat denatured RNA on polyacrylamide–urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncRNAs of interest.

The larva of Hydropsyche doehleri Tobias 1972, based on Swiss material (Hydropsychidae, Trichoptera)

Zootaxa ◽  
2020 ◽  
Vol 4786 (4) ◽  
pp. 535-545
Author(s):  
HEINRICH VICENTINI ◽  
SOFIA WYLER ◽  
JOHANN WARINGER
Keyword(s):  
Abdominal Segment ◽  
Sequence Data ◽  
Light Trap ◽  
Distribution Patterns ◽  
Adult Males ◽  
Diagnostic Features ◽  
Species Association ◽  
Dna Sequence Data ◽  
Males And Females ◽  
Region Information

This paper describes the previously unknown larva of Hydropsyche doehleri Tobias 1972. Species association was enabled by the fact that both larval and adult specimens were collected at the same location and that H. doehleri was the only Hydropsychidae collected at this site, based on light-trap samples of adults. In addition, association of larvae with adult males and females were performed using DNA sequence data from the mitochondrial cytochrome c oxidase region. Information on the morphology of the larva is given, and the most important diagnostic features separating H. doehleri from its sister taxon H. siltalai Döhler 1963 are discussed. In both species, gills are lacking on abdominal segment VII. In the context of the Hydropsychidae key of Waringer & Graf (2011), the two species can be separated by the morphology and coloration of the frontoclypeal apotome, and by their distribution patterns: whereas H. siltalai is widespread in Europe, H. doehleri has been reported from only France, Italy, and southern Switzerland (Tessin).                #We dedicate this paper to Univ. Prof. Dr Hans Malicky on the occasion of his 85th birthday. 

Molecular characterization of two insect nematode species (Oxyurida: Thelastomatidae) using small subunit (18S) ribosomal DNA sequence and secondary-structure analyses

2013 ◽  
Vol 88 (2) ◽  
pp. 219-229
Author(s):  
A. Chaudhary ◽  
N. Singh ◽  
H.S. Singh
Keyword(s):  
Secondary Structure ◽  
Molecular Characterization ◽  
Ribosomal Dna ◽  
Periplaneta Americana ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nematode Species ◽  
Small Subunit ◽  
Primary Sequence ◽  
Primary Sequence Data

AbstractNematodes of the family Thelastomatidae are parasitic in the alimentary tract of many arthropods, including Periplaneta americana L. In Meerut, Uttar Pradesh, India, two nematode species, namely Hammerschmidtiella indicus and Thelastoma icemi, belonging to this family have been reported. In the present study, the molecular phylogeny of these two nematode species was derived using small subunit (18S) sequence and secondary-structure analyses. The small subunit sequence analyses were carried out to explore the validation and systematics of these species. Phylogenetic analyses were performed for primary sequence data as well as using neighbour-joining and maximum-parsimony approaches. In contrast, the inferred secondary structures for the two species, using free-energy modelling, showed structural identities. As well as this, motif sequences were also found to be a promising tool for nematode species identification. The study provides molecular characterization based on primary sequence data of the 18S ribosomal DNA region of the nematodes along with secondary-structure data and motif sequences for inferences at higher taxonomic levels.

scholarly journals Comparative analysis of full-length antigen II/3 fromEchinococcus multilocularisandE. granulosus

Parasitology ◽  
1994 ◽  
Vol 109 (2) ◽  
pp. 223-232 ◽  
Author(s):  
R. Felleisen ◽  
B. Gottstein
Keyword(s):  
Cystic Echinococcosis ◽  
Alveolar Echinococcosis ◽  
Sequence Data ◽  
Pcr Amplification ◽  
Full Length ◽  
Primary Sequence ◽  
Glutathione S Transferase ◽  
Gene Encoding ◽  
Nucleotide Sequence Data ◽  
Binding Characteristics

SUMMARYThe recombinantEchinococcus multilocularisantigen ll/3–10 is one of the most promising tools for immunodiagnosis of alveolar echinococcosis in human patients. Its nucleic acid sequence represents a part of theE. multilocularisgene encoding the metacestode antigen II/3, the former being basically present and expressed in bothE. multilocularisandE. granulosus. Most (94%) patients with alveolar echinococcosis respond to infection with a marked anti-II/3–10 IgG synthesis; in contrast, most of the cystic echinococcosis patients do not, for some reason, recognize the recombinant antigen. We tackled this problem by generating cDNA derived from bothE. granulosusandE. multilocularisfull length II/3 genes, performed by reverse transcription and PCR amplification. Sequence analysis revealed a very high degree of conservation of the primary sequence of the antigen II/3 in bothEchinococcusspecies. cDNA fragments were subcloned and expressed inE. colias fusion proteins withSchistosoma japonicumglutathione S-transferase. Recombinant proteins were affinity purified and comparatively assessed by ELISA with respect to antibody-binding characteristics. Sera from patients suffering from cystic echinococcosis showed no significant differences in reactivity with the antigens derived from eitherE. multilocularisorE. granulosus. Therefore, parameters other than some minor differences in the primary sequence seem to be responsible for the lack of antigen II/3 recognition in cystic echinococcosis.NoteNucleotide sequence data reported in this paper have been submitted to the GenBank®data base with the accession numbers U05573 and U05574.

scholarly journals Nudivirus Sequences Identified from the Southern and Western Corn Rootworms (Coleoptera: Chrysomelidae)

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 269
Author(s):  
Sijun Liu ◽  
Thomas W. Sappington ◽  
Brad S. Coates ◽  
Bryony C. Bonning
Keyword(s):  
Genome Sequence ◽  
Insect Pests ◽  
Sequence Data ◽  
Diabrotica Virgifera Virgifera ◽  
Open Reading Frames ◽  
Corn Rootworm ◽  
Geographically Dispersed ◽  
Diabrotica Undecimpunctata Howardi ◽  
Short Read Sequence ◽  
Core Genes

Analysis of pooled genomic short read sequence data revealed the presence of nudivirus-derived sequences from U.S. populations of both southern corn rootworm (SCR, Diabrotica undecimpunctata howardi Barber) and western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte). A near complete nudivirus genome sequence was assembled from sequence data for an SCR population with relatively high viral titers. A total of 147,179 bp was assembled from five contigs that collectively encode 109 putative open reading frames (ORFs) including 20 nudivirus core genes. In contrast, genome sequence recovery was incomplete for a second nudivirus from WCR, although sequences derived from this virus were present in three geographically dispersed populations. Only 48,989 bp were assembled with 48 putative ORFs including 13 core genes, representing about 20% of a typical nudivirus genome. Phylogenetic analysis indicated that both corn rootworm nudiviruses grouped with the third known nudivirus of beetles, Oryctes rhinoceros nudivirus in the genus Alphanudivirus. On the basis of phylogenetic and additional analyses, we propose further taxonomic separation of nudiviruses within Alphanudivirus and Betanudivirus into two subfamilies and five genera. Identification of nudivirus-derived sequences from two species of corn rootworm highlights the diversity of viruses associated with these agricultural insect pests.

scholarly journals Predicting Antimicrobial Resistance Using Conserved Genes

2020 ◽  
Author(s):  
Marcus Nguyen ◽  
Robert Olson ◽  
Maulik Shukla ◽  
Margo VanOeffelen ◽  
James J. Davis
Keyword(s):  
Machine Learning ◽  
Antimicrobial Resistance ◽  
Sequence Data ◽  
Core Gene ◽  
Error Rates ◽  
Machine Learning Algorithms ◽  
Major Error ◽  
Building Models ◽  
Conserved Genes ◽  
Core Genes

AbstractA growing number of studies have shown that machine learning algorithms can be used to accurately predict antimicrobial resistance (AMR) phenotypes from bacterial sequence data. In these studies, models are typically trained using input features derived from comprehensive sets of known AMR genes or whole genome sequences. However, it can be difficult to determine whether genomes and their corresponding sets of AMR genes are complete when sequencing contaminated or metagenomic samples. In this study, we explore the possibility of using incomplete genome sequence data to predict AMR phenotypes. Machine learning models were built from randomly-selected sets of core genes that are held in common among the members of a species, and the AMR-conferring genes were removed based on their protein annotations. For Klebsiella pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, and Staphylococcus aureus, we report that it is possible to classify susceptible and resistant phenotypes with average F1 scores ranging from 0.80-0.89 with as few as 100 conserved non-AMR genes, with very major error rates ranging from 0.11-0.23 and major error rates ranging from 0.10-0.20. Models built from core genes have predictive power in the cases where the primary AMR mechanism results from SNPs or horizontal gene transfer. By randomly sampling non-overlapping sets of core genes for use in these models, we show that F1 scores and error rates are stable and have little variance between replicates. Potential biases from strain-specific SNPs, phylogenetic sampling, and imbalances in the phylogenetic distribution of susceptible and resistant strains do not appear to have an impact on this result. Although these small core gene models have lower accuracies and higher error rates than models built from the corresponding assembled genomes, the results suggest that sufficient variation exists in the core non-AMR genes of a species for predicting AMR phenotypes. Overall this study suggests that building models from conserved genes may be a potentially useful strategy for predicting AMR phenotypes when genomes are incomplete.

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