scholarly journals Killer Knots: Molecular evolution of Inhibitor Cystine Knot toxins in wandering spiders (Araneae: Ctenidae)

2021 ◽  
Author(s):  
T. Jeffrey Cole ◽  
Michael S Brewer
Keyword(s):  
Negative Selection ◽  
Large Fraction ◽  
Venom Gland ◽  
Functional Diversification ◽  
Evolutionary Patterns ◽  
Cystine Knot ◽  
Agricultural Applications ◽  
Close Relatives ◽  
Functionally Diverse ◽  
Phoneutria Nigriventer

Venom expressed by the nearly 50,000 species of spiders on Earth largely remains an untapped reservoir of a diverse array of biomolecules with potential for pharmacological and agricultural applications. A large fraction of the noxious components of spider venoms are a functionally diverse family of structurally related polypeptides with an inhibitor cystine knot (ICK) motif. The cysteine-rich nature of these toxins makes structural elucidation difficult, and most studies have focused on venom components from the small handful of medically relevant spider species such as the highly aggressive Brazilian wandering spider Phoneutria nigriventer. To alleviate difficulties associated with the study of ICK toxins in spiders, we devised a comprehensive approach to explore the evolutionary patterns that have shaped ICK functional diversification using venom gland transcriptomes and proteomes from phylogenetically distinct lineages of wandering spiders and their close relatives. We identified 626 unique ICK toxins belonging to seven topological elaborations. Phylogenetic tests of episodic diversification revealed distinct regions between cysteine residues that demonstrated differential evidence of positive or negative selection, which may have structural implications towards the specificity and efficacy of these toxins. Increased taxon sampling and whole genome sequencing will provide invaluable insights to further understand the evolutionary processes that have given rise to this diverse class of toxins.

scholarly journals Description and evolution of wood anatomical characters in the ebony wood genus Diospyros and its close relatives (Ebenaceae): a first step towards combatting illegal logging

IAWA Journal ◽  
2020 ◽  
Vol 41 (4) ◽  
pp. 577-619 ◽  
Author(s):  
Mehrdad Jahanbanifard ◽  
Vicky Beckers ◽  
Gerald Koch ◽  
Hans Beeckman ◽  
Barbara Gravendeel ◽  
...  
Keyword(s):  
Identification Accuracy ◽  
Reference Database ◽  
Ancestral State ◽  
Evolutionary Patterns ◽  
Chemical Profiling ◽  
The Family ◽  
Anatomical Characters ◽  
Perforation Plates ◽  
Close Relatives ◽  
Local Deposition

Abstract The typical black coloured ebony wood (Diospyros, Ebenaceae) is desired as a commercial timber because of its durable and aesthetic properties. Surprisingly, a comprehensive wood anatomical overview of the genus is lacking, making it impossible to fully grasp the diversity in microscopic anatomy and to distinguish between CITES protected species native to Madagascar and the rest. We present the largest microscopic wood anatomical reference database for ebony woods and reconstruct evolutionary patterns in the microscopic wood anatomy within the family level using an earlier generated molecular phylogeny. Wood samples from 246 Diospyros species are described based on standardised light microscope observations. For the ancestral state reconstruction, we selected eight wood anatomical characters from 88 Ebenaceae species (including 29 Malagasy Diospyros species) that were included in the most recently reconstructed family phylogeny. Within Diospyros, the localisation of prismatic crystals (either in axial parenchyma or in rays) shows the highest phylogenetic value and appears to have a biogeographical signal. The molecular defined subclade Diospyros clade IX can be clearly distinguished from other ebony woods by its storied structure. Across Ebenaceae, Lissocarpa is distinguishable from the remaining genera by the combined presence of scalariform and simple vessel perforation plates, and Royena typically has silica bodies instead of prismatic crystals. The local deposition of prismatic crystals and the presence of storied structure allow identifying ebony wood species at the subgeneric level, but species-level identification is not possible. In an attempt to improve the identification accuracy of the CITES protected Malagasy woods, we applied computer vision algorithms based on microscopic images from our reference database (microscopic slides from ca. 1000 Diospyros specimens) and performed chemical profiling based on DART TOFMS.

scholarly journals Thymic negative selection is functional in NOD mice

2012 ◽  
Vol 209 (3) ◽  
pp. 623-637 ◽  
Author(s):  
Michael Mingueneau ◽  
Wenyu Jiang ◽  
Markus Feuerer ◽  
Diane Mathis ◽  
Christophe Benoist
Keyword(s):  
Genetic Variation ◽  
Negative Selection ◽  
Biochemical Analysis ◽  
Large Fraction ◽  
Nod Mice ◽  
Double Positive ◽  
Clonal Deletion ◽  
Nonobese Diabetic ◽  
Early Expression ◽  
Bone Marrow Chimeras

Based on analyses of multiple TCR transgenic (tg) models, the emergence of pathogenic T cells in diabetes-prone NOD mice has been ascribed to a failure to censure autoreactive clones in the thymus. In contrast, using isolated and preselected thymocytes, we show that nonobese diabetic (NOD) genetic variation impairs neither clonal deletion nor downstream transcriptional programs. However, we find that NOD genetic variation influences αβ/γδ-lineage decisions promoted by early expression of tg αβ-TCRs at the double-negative (DN) stage. In B6 and other genetic backgrounds, tg αβ-TCRs behave like γδ-TCRs and commit a large fraction of DNs toward the γδ-lineage, thereby decreasing the size of the double-positive (DP) pool, which is efficiently positively and negatively selected. In NOD DNs, αβ-TCR signalosomes instead behave like pre-TCRs, resulting in high numbers of DPs competing for limited selection niches, and poor positive and negative selection. Once niche effects are neutralized in mixed bone marrow chimeras, positive and negative selection are equally efficient on B6 and NOD backgrounds. Biochemical analysis revealed a selective defect in the activation of Erk1/2 downstream of NOD αβ-TCR signalosomes. Therefore, NOD genetic variation influences αβ/γδ-lineage decisions when the αβ-TCR heterodimer is prematurely expressed, but not the process of negative selection.

scholarly journals Mining Indole Alkaloid Synthesis Gene Clusters from Genomes of 53 Claviceps Strains Revealed Redundant Gene Copies and an Approximate Evolutionary Hourglass Model

Toxins ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 799
Author(s):  
Miao Liu ◽  
Wendy Findlay ◽  
Jeremy Dettman ◽  
Stephen A. Wyka ◽  
Kirk Broders ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Wide Spectrum ◽  
Ergot Alkaloids ◽  
Indole Alkaloid ◽  
Gene Clusters ◽  
Evolutionary Patterns ◽  
Beneficial Effects ◽  
Gene Copies ◽  
Hourglass Model ◽  
Close Relatives

Ergot fungi (Claviceps spp.) are infamous for producing sclerotia containing a wide spectrum of ergot alkaloids (EA) toxic to humans and animals, making them nefarious villains in the agricultural and food industries, but also treasures for pharmaceuticals. In addition to three classes of EAs, several species also produce paspaline-derived indole diterpenes (IDT) that cause ataxia and staggers in livestock. Furthermore, two other types of alkaloids, i.e., loline (LOL) and peramine (PER), found in Epichloë spp., close relatives of Claviceps, have shown beneficial effects on host plants without evidence of toxicity to mammals. The gene clusters associated with the production of these alkaloids are known. We examined genomes of 53 strains of 19 Claviceps spp. to screen for these genes, aiming to understand the evolutionary patterns of these genes across the genus through phylogenetic and DNA polymorphism analyses. Our results showed (1) varied numbers of eas genes in C. sect. Claviceps and sect. Pusillae, none in sect. Citrinae, six idt/ltm genes in sect. Claviceps (except four in C. cyperi), zero to one partial (idtG) in sect. Pusillae, and four in sect. Citrinae, (2) two to three copies of dmaW, easE, easF, idt/ltmB, itd/ltmQ in sect. Claviceps, (3) frequent gene gains and losses, and (4) an evolutionary hourglass pattern in the intra-specific eas gene diversity and divergence in C. purpurea.

scholarly journals Functional diversity of small-mammal postcrania is linked to both substrate preference and body size

2020 ◽  
Vol 66 (5) ◽  
pp. 539-553
Author(s):  
Lucas N Weaver ◽  
David M Grossnickle
Keyword(s):  
Body Size ◽  
Phenotypic Diversity ◽  
Small Body ◽  
Ecological Factors ◽  
Morphological Divergence ◽  
Functional Diversification ◽  
Evolutionary Patterns ◽  
Selective Pressures ◽  
Trade Offs ◽  
Body Sizes

Abstract Selective pressures favor morphologies that are adapted to distinct ecologies, resulting in trait partitioning among ecomorphotypes. However, the effects of these selective pressures vary across taxa, especially because morphology is also influenced by factors such as phylogeny, body size, and functional trade-offs. In this study, we examine how these factors impact functional diversification in mammals. It has been proposed that trait partitioning among mammalian ecomorphotypes is less pronounced at small body sizes due to biomechanical, energetic, and environmental factors that favor a “generalist” body plan, whereas larger taxa exhibit more substantial functional adaptations. We title this the Divergence Hypothesis (DH) because it predicts greater morphological divergence among ecomorphotypes at larger body sizes. We test DH by using phylogenetic comparative methods to examine the postcranial skeletons of 129 species of taxonomically diverse, small-to-medium-sized (<15 kg) mammals, which we categorize as either “tree-dwellers” or “ground-dwellers.” In some analyses, the morphologies of ground-dwellers and tree-dwellers suggest greater between-group differentiation at larger sizes, providing some evidence for DH. However, this trend is neither particularly strong nor supported by all analyses. Instead, a more pronounced pattern emerges that is distinct from the predictions of DH: within-group phenotypic disparity increases with body size in both ground-dwellers and tree-dwellers, driven by morphological outliers among “medium”-sized mammals. Thus, evolutionary increases in body size are more closely linked to increases in within-locomotor-group disparity than to increases in between-group disparity. We discuss biomechanical and ecological factors that may drive these evolutionary patterns, and we emphasize the significant evolutionary influences of ecology and body size on phenotypic diversity.

Specialisation of the Venom Gland Proteome in Predatory Cone Snails Reveals Functional Diversification of the Conotoxin Biosynthetic Pathway

2011 ◽  
Vol 10 (9) ◽  
pp. 3904-3919 ◽  
Author(s):  
Helena Safavi-Hemami ◽  
William A. Siero ◽  
Dhana G. Gorasia ◽  
Neil D. Young ◽  
David MacMillan ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Venom Gland ◽  
Functional Diversification ◽  
Cone Snails

scholarly journals Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Vladimir Makarenkov ◽  
Bogdan Mazoure ◽  
Guillaume Rabusseau ◽  
Pierre Legendre
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Intermediate Host ◽  
Close Relative ◽  
Intragenic Recombination ◽  
Recombination Analysis ◽  
Gene Trees ◽  
Intermediate Hosts ◽  
Evolutionary Patterns ◽  
Close Relatives

Abstract Background The SARS-CoV-2 pandemic is one of  the greatest  global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. Results We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215–1425] of gene S and region [534–727] of gene N. Moreover, some statistically significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. Conclusions The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of this dangerous virus. 

scholarly journals Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

2020 ◽  
Author(s):  
Vladimir Makarenkov ◽  
Bogdan Mazoure ◽  
Guillaume Rabusseau ◽  
Pierre Legendre
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Intermediate Host ◽  
Close Relative ◽  
Intragenic Recombination ◽  
Recombination Analysis ◽  
Gene Trees ◽  
Intermediate Hosts ◽  
Evolutionary Patterns ◽  
Close Relatives

AbstractBackgroundThe SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein.ResultsWe provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-Cov-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215-1425] of gene S and region [534-727] of gene N. Moreover, some significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster.ConclusionsThe results of our horizontal gene transfer and recombination analysis suggest that SARS-Cov-2 could not only be a chimera resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of SARS-CoV-2.

scholarly journals Comparative metagenomics of coalbed methane microbial communities reveals biogenic methane potential in the Appalachian Basin

2018 ◽  
Author(s):  
Daniel E. Ross ◽  
Daniel Lipus ◽  
Kelvin B. Gregory ◽  
Djuna Gulliver
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
Coalbed Methane ◽  
Large Fraction ◽  
Appalachian Basin ◽  
Well Performance ◽  
Biogenic Methane ◽  
Comparative Metagenomics ◽  
Functionally Diverse ◽  
High Degree

Natural gas is a major source of global energy, and a large fraction is generated in subsurface coalbed deposits. Microbial communities within coalbed deposits impact methane production, and as a result contribute to global carbon cycling. The process of biogenic coal-to-methane conversion is not well understood. Here we demonstrate the first read- and assembly-based metagenome profiling of coal-associated formation waters, resulting in the recovery of over 40 metagenome-assembled genomes (MAGs) from eight individual coalbed methane wells in the Appalachian Basin. The majority of samples contained hydrogenotrophic methanogens, which were present in higher relative abundances than was previously reported for other coalbed basins. The abundance of Archaea and salinity were positively correlated, suggesting that salinity may be a controlling factor for biogenic coalbed methane. Low-abundance coalbed microbial populations were functionally diverse, while the most dominant organisms exhibit a high degree of genomic and functional similarities. Basin-specific pan-metagenome clustering suggests lower abundant and diverse bacterial communities are shaped by local basin parameters. Our analyses show Appalachian Basin coalbed microbial communities encode for the potential to convert coal into methane, which may be used as an indicator of potential biogenic methane production for future well performance and increased well longevity.

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