Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

Abstract Background K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors. Results For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile. Conclusion This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.

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On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn’t

Genes ◽

10.3390/genes12040527 ◽

2021 ◽

Vol 12 (4) ◽

pp. 527

Author(s):

Eran Elhaik ◽

Dan Graur

Keyword(s):

Machine Learning ◽

Learning Algorithm ◽

A Priori ◽

Neutral Theory ◽

Dominant Mode ◽

Supervised Machine Learning ◽

Training Dataset ◽

Selective Sweeps ◽

Two Factors ◽

Negative Controls

In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transformation was aided by a series of articles by Daniel Schrider and Andrew Kern. Within this series, a paper entitled “Soft sweeps are the dominant mode of adaptation in the human genome” (Schrider and Kern, Mol. Biol. Evolut. 2017, 34(8), 1863–1877) attracted a great deal of attention, in particular in conjunction with another paper (Kern and Hahn, Mol. Biol. Evolut. 2018, 35(6), 1366–1371), for purporting to discredit the Neutral Theory of Molecular Evolution (Kimura 1968). Here, we address an alleged novelty in Schrider and Kern’s paper, i.e., the claim that their study involved an artificial intelligence technique called supervised machine learning (SML). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known empirically to be true. Curiously, Schrider and Kern did not possess a training dataset of genomic segments known a priori to have evolved either neutrally or through soft or hard selective sweeps. Thus, their claim of using SML is thoroughly and utterly misleading. In the absence of legitimate training datasets, Schrider and Kern used: (1) simulations that employ many manipulatable variables and (2) a system of data cherry-picking rivaling the worst excesses in the literature. These two factors, in addition to the lack of negative controls and the irreproducibility of their results due to incomplete methodological detail, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., S/HIC) should be taken with a huge shovel of salt.

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Economic and IT determinants of innovative projects in the textiles, wearing apparel, leather and related products industry

Industria Textila ◽

10.35530/it.069.04.1478 ◽

2018 ◽

Vol 69 (04) ◽

pp. 338-344

Author(s):

SIMION CEZAR-PETRE ◽

ALEXANDRU ADRIANA ◽

CEPTUREANU SEBASTIAN ION ◽

CEPTUREANU EDUARD GABRIEL

Keyword(s):

European Union ◽

Correlation Analysis ◽

Volume Index ◽

Major Influence ◽

Factors Influencing ◽

Global Demand ◽

Two Factors ◽

Main Factors ◽

Potential Factors

In this paper the main factors that influence the innovative projects in the field of textiles, wearing apparel, leather and related products were identified and analyzed. Eleven potential factors influencing innovative projects have been considered and the correlation analysis has identified the two factors that have a major influence on innovative projects in the field: volume index of production in European Union for NACE codes 13-15 and exports value for textiles, wearing apparel, leather and related products. The research has shown that the scale of innovative projects in textiles, clothing, leather and related products depends on European Union production and on global demand.

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Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

10.20944/preprints201810.0596.v1 ◽

2018 ◽

Author(s):

Marine Lambert ◽

Abderrahim Benmoussa ◽

Patrick Provost

Keyword(s):

Ribosomal Rna ◽

Potential Role ◽

A Priori ◽

Biological Significance ◽

Rna Seq ◽

New Class ◽

Scientific Mind ◽

Non Coding Rnas ◽

And Function ◽

Rrna Sequences

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

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DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

International Journal of Molecular Sciences ◽

10.3390/ijms20133349 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3349 ◽

Cited By ~ 5

Author(s):

Jose María Miralles-Robledillo ◽

Javier Torregrosa-Crespo ◽

Rosa María Martínez-Espinosa ◽

Carmen Pire

Keyword(s):

Redox Reactions ◽

Molecular Mechanisms ◽

Biological Significance ◽

Anaerobic Respiration ◽

Biogeochemical Cycles ◽

Free Software ◽

Transfer Processes ◽

Expression Of Genes ◽

Potential Applications ◽

Domains Of Life

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.

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Complete Genome Sequence of the Anaerobic, Protein-Degrading Hyperthermophilic Crenarchaeon Desulfurococcus kamchatkensis

Journal of Bacteriology ◽

10.1128/jb.01525-08 ◽

2008 ◽

Vol 191 (7) ◽

pp. 2371-2379 ◽

Cited By ~ 32

Author(s):

Nikolai V. Ravin ◽

Andrey V. Mardanov ◽

Alexey V. Beletsky ◽

Ilya V. Kublanov ◽

Tatiana V. Kolganova ◽

...

Keyword(s):

Hot Spring ◽

Genome Structure ◽

Nucleotide Composition ◽

Mobile Elements ◽

Circular Chromosome ◽

Extrachromosomal Elements ◽

Single Region ◽

Genes Encoding ◽

Multiple Copies ◽

Modified Embden Meyerhof Pathway

ABSTRACT Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extrachromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for D. kamchatkensis. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS607 and IS200/IS605 families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of D. kamchatkensis. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.

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Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0033 ◽

2009 ◽

Vol 364 (1527) ◽

pp. 2229-2239 ◽

Cited By ~ 49

Author(s):

Gregory P. Fournier ◽

Jinling Huang ◽

J. Peter Gogarten

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Phylogenetic Reconstruction ◽

Gene Trees ◽

Individual Gene ◽

Evolution Of Life ◽

Domains Of Life ◽

Life On Earth ◽

Simple Tree

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

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Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis

10.1101/2020.04.16.045138 ◽

2020 ◽

Author(s):

Javier M. González

Keyword(s):

Redox Reactions ◽

Sequence Similarity ◽

Phylogenetic Reconstruction ◽

Transition Metal Ions ◽

Sequence Annotation ◽

Connectivity Analysis ◽

Topological Properties ◽

Structural Homology ◽

Similarity Network ◽

Domains Of Life

ABSTRACTThe superfamily of metallo-β-lactamases (MBL) comprises an ancient group of proteins found in all domains of life, sharing a characteristic αββα fold and a histidine-rich motif for binding of transition metal ions, with the ability to catalyze a variety of hydrolysis and redox reactions. Herein, structural homology and sequence similarity network (SSN) analysis are used to assist the phylogenetic reconstruction of the MBL superfamily, introducing tanglegrams to evaluate structure-function relationships. SSN neighborhood connectivity is applied for spotting protein families within SSN clusters, showing that 98 % of the superfamily remains to be explored experimentally. Further SSN research is suggested in order to determine their topological properties, which will be instrumental for the improvement of automated sequence annotation methods.

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The Hypercomplex Genome of an Insect Reproductive Parasite Highlights the Importance of Lateral Gene Transfer in Symbiont Biology

mBio ◽

10.1128/mbio.02590-19 ◽

2020 ◽

Vol 11 (2) ◽

Author(s):

Crystal L. Frost ◽

Stefanos Siozios ◽

Pol Nadal-Jimenez ◽

Michael A. Brockhurst ◽

Kayla C. King ◽

...

Keyword(s):

Parasitic Wasp ◽

Genetic Material ◽

Mobile Elements ◽

Bacterial Genomes ◽

Nasonia Vitripennis ◽

Content Type ◽

Microbial Function ◽

Extrachromosomal Elements ◽

Long Read ◽

Genomic Regions

ABSTRACT Mobile elements—plasmids and phages—are important components of microbial function and evolution via traits that they encode and their capacity to shuttle genetic material between species. We here report the unusually rich array of mobile elements within the genome of Arsenophonus nasoniae, the son-killer symbiont of the parasitic wasp Nasonia vitripennis. This microbe’s genome has the highest prophage complement reported to date, with over 50 genomic regions that represent either intact or degraded phage material. Moreover, the genome is predicted to include 17 extrachromosomal genetic elements, which carry many genes predicted to be important at the microbe-host interface, derived from a diverse assemblage of insect-associated gammaproteobacteria. In our system, this diversity was previously masked by repetitive mobile elements that broke the assembly derived from short reads. These findings suggest that other complex bacterial genomes will be revealed in the era of long-read sequencing. IMPORTANCE The biology of many bacteria is critically dependent on genes carried on plasmid and phage mobile elements. These elements shuttle between microbial species, thus providing an important source of biological innovation across taxa. It has recently been recognized that mobile elements are also important in symbiotic bacteria, which form long-lasting interactions with their host. In this study, we report a bacterial symbiont genome that carries a highly complex array of these elements. Arsenophonus nasoniae is the son-killer microbe of the parasitic wasp Nasonia vitripennis and exists with the wasp throughout its life cycle. We completed its genome with the aid of recently developed long-read technology. This assembly contained over 50 chromosomal regions of phage origin and 17 extrachromosomal elements within the genome, encoding many important traits at the host-microbe interface. Thus, the biology of this symbiont is enabled by a complex array of mobile elements.

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Coupling phases and amplitudes of minor constituents with temperature perturbations in the lower thermosphere

Annales Geophysicae ◽

10.1007/s00585-994-0438-0 ◽

1994 ◽

Vol 12 (5) ◽

pp. 438-447

Author(s):

Y. W. Chen ◽

F. L. Xiao

Keyword(s):

Lower Thermosphere ◽

Scale Height ◽

Rate Coefficients ◽

Major Constituent ◽

Major Influence ◽

Temperature Perturbation ◽

Minor Constituents ◽

Two Factors ◽

Atmospheric Gravity ◽

Density Scale

Abstract. Based on the linearized theory of atmospheric gravity waves (AGW) and considering the effects of temperature perturbation on the chemical rate coefficients, the formulae of coupling relations between nj/nj and T'/T driven by AGW (nj and T denote the background quantities) are described, the coupling phases and amplitudes of minor constituents O3, NO, H, OH, and O are analyzed in detail for the mesopause (86 km) and just upside of the O layer (100 km) at daytime. A general principle is outlined: the coupling phases are strongly dependent on density scale heights and perturbation scales, while the amplitudes are little affected by these two factors. A criterion to distinguish the coupling behaviour is given: when the minor constituent number density scale height Hj satisfies 1-γHm/Hj>0 (Hm denotes the scale height of the major constituent), the dynamical perturbation process always keeps the nj/nj in phase with T'/T, i.e. keeps the nj/nj in antiphase with that of the major constituent. The results obtained indicate that both the temperature dependence of reaction rate coefficients and the profile slopes of the O distribution may have a major influence on the behaviour of the coupling relations.

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Phylogeny of the Oxycoryninae sensu lato (Coleoptera:Belidae) and evolution of host-plant associations

Invertebrate Systematics ◽

10.1071/is05059 ◽

2006 ◽

Vol 20 (4) ◽

pp. 447 ◽

Cited By ~ 25

Author(s):

A. E. Marvaldi ◽

R. G. Oberprieler ◽

C. H. C. Lyal ◽

T. Bradbury ◽

R. S. Anderson

Keyword(s):

Host Plants ◽

Feeding Habits ◽

Phylogenetic Reconstruction ◽

Cladistic Analysis ◽

Major Influence ◽

Biological Traits ◽

Larval Feeding ◽

Plant Associations ◽

New Information

Phylogenetic relationships among the genera of the subfamily Oxycoryninae and other belids (Curculionoidea) were reconstructed by cladistic analysis using 21 terminals and 98 characters: 62 from imaginal morphology, 33 from larval morphology and three biological characters relating to host plants and larval feeding habits. Terminal taxa represent all extant genera of Oxycoryninae, two genera of each of the three tribes of Belinae plus two outgroup taxa used to root the tree. New information on the larvae and biology of the metrioxenines is used in phylogenetic reconstruction. In accord with the single optimal cladogram obtained, a revised classification of the Oxycoryninae is proposed. The subfamily is classified into three tribes (Oxycorynini, Metrioxenini and Aglycyderini), with the tribe Oxycorynini further classified into three subtribes (Oxycraspedina Marvaldi & Oberprieler, subtr. nov., Oxycorynina and Allocorynina) and the tribe Metrioxenini into two subtribes (Metrioxenina and Afrocorynina ( = Hispodini, syn. nov.)). Larval and adult unambiguous synapomorphies defining each clade are identified. Tracing the evolution of biological traits from the phylogenetic estimate indicates that drastic shifts to phylogenetically distant host plants occurred from the ancestral belid association with conifers. Structural, chemical and/or ecological similarities of the plant organs consumed apparently had a major influence in the colonisation of different plant taxa by this group of weevils.

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