scholarly journals Pick Your Poison: Molecular Evolution of Venom Proteins in Asilidae (Insecta: Diptera)

Toxins ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 738
Author(s):  
Chris M. Cohen ◽  
T. Jeffrey Cole ◽  
Michael S. Brewer
Keyword(s):  
Salivary Gland ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Negative Selection ◽  
Gene Families ◽  
Whole Body ◽  
Robber Flies ◽  
First Time ◽  
Venom Proteins

Robber flies are an understudied family of venomous, predatory Diptera. With the recent characterization of venom from three asilid species, it is possible, for the first time, to study the molecular evolution of venom genes in this unique lineage. To accomplish this, a novel whole-body transcriptome of Eudioctria media was combined with 10 other publicly available asiloid thoracic or salivary gland transcriptomes to identify putative venom gene families and assess evidence of pervasive positive selection. A total of 348 gene families of sufficient size were analyzed, and 33 of these were predicted to contain venom genes. We recovered 151 families containing homologs to previously described venom proteins, and 40 of these were uniquely gained in Asilidae. Our gene family clustering suggests that many asilidin venom gene families are not natural groupings, as delimited by previous authors, but instead form multiple discrete gene families. Additionally, robber fly venoms have relatively few sites under positive selection, consistent with the hypothesis that the venoms of older lineages are dominated by negative selection acting to maintain toxic function.

scholarly journals Pick Your Poison: Molecular Evolution of Venom Proteins in Asilidae (Insecta: Diptera)

2020 ◽  
Author(s):  
Chris M. Cohen ◽  
T. Jeffrey Cole ◽  
Michael S. Brewer
Keyword(s):  
Salivary Gland ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Negative Selection ◽  
Gene Families ◽  
Whole Body ◽  
Robber Flies ◽  
First Time ◽  
Venom Proteins

AbstractRobber flies are an understudied family of venomous, predatory Diptera. With the recent characterization of venom from three asilid species, it is possible for the first time to study the molecular evolution of venom genes in this unique lineage. To accomplish this, a novel whole-body transcriptome of Eudioctria media was combined with 10 other publicly available asiloid thoracic or salivary gland transcriptomes to identify putative venom gene families and assess evidence of pervasive positive selection. A total of 348 gene families of sufficient size were analyzed, and 33 of these were predicted to contain venom genes. We recovered 151 families containing homologs to previously described venoms, and 40 of these were uniquely gained in Asilidae. Our gene family clustering suggests that many asilidin venom gene families are not natural groupings as originally delimited. Additionally, robber-fly venoms have relatively few sites under positive selection, consistent with the hypothesis that the venom of older lineages are dominated by negative selection acting to maintain toxic function.

scholarly journals Proteo-Transcriptomic Characterization of the Venom from the Endoparasitoid Wasp Pimpla turionellae with Aspects on Its Biology and Evolution

Toxins ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 721 ◽  
Author(s):  
Rabia Özbek ◽  
Natalie Wielsch ◽  
Heiko Vogel ◽  
Günter Lochnit ◽  
Frank Foerster ◽  
...  
Keyword(s):  
Transcriptome Assembly ◽  
Parasitoid Wasp ◽  
Venom Gland ◽  
Hymenopteran Species ◽  
Robber Flies ◽  
And Function ◽  
Wasp Venoms ◽  
Venom Proteins ◽  
Proteins And Peptides

Within mega-diverse Hymenoptera, non-aculeate parasitic wasps represent 75% of all hymenopteran species. Their ovipositor dual-functionally injects venom and employs eggs into (endoparasitoids) or onto (ectoparasitoids) diverse host species. Few endoparasitoid wasps such as Pimpla turionellae paralyze the host and suppress its immune responses, such as encapsulation and melanization, to guarantee their offspring’s survival. Here, the venom and its possible biology and function of P. turionellae are characterized in comparison to the few existing proteo-transcriptomic analyses on parasitoid wasp venoms. Multiple transcriptome assembly and custom-tailored search and annotation strategies were applied to identify parasitoid venom proteins. To avoid false-positive hits, only transcripts were finally discussed that survived strict filter settings, including the presence in the proteome and higher expression in the venom gland. P. turionella features a venom that is mostly composed of known, typical parasitoid enzymes, cysteine-rich peptides, and other proteins and peptides. Several venom proteins were identified and named, such as pimplin2, 3, and 4. However, the specification of many novel candidates remains difficult, and annotations ambiguous. Interestingly, we do not find pimplin, a paralytic factor in Pimpla hypochondriaca, but instead a new cysteine inhibitor knot (ICK) family (pimplin2), which is highly similar to known, neurotoxic asilid1 sequences from robber flies.

scholarly journals Positive selection in multiple salivary gland proteins of Anophelinae reveals potential targets for vector control

2021 ◽  
Author(s):  
Lucas Freitas ◽  
Mariana F. Nery
Keyword(s):  
Salivary Gland ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Feeding Behavior ◽  
Vector Control ◽  
Copy Number ◽  
Blood Feeding ◽  
Evolution Analysis ◽  
New Strategies ◽  
Positively Selected Sites

AbstractAnopheles is a genus belonging to the Culicidae family, which has great medical importance due to its role as a vector of Plasmodium, the parasite responsible for malaria. From Anopheles’ functional genomics, great focus has been given to the salivary gland proteins (SGPs) group. This class of proteins is essential to blood-feeding behavior as they have attributes such as vasodilators and anti-clotting properties. Recently, a comprehensive review on Anopheles SGPs was performed, however the authors did not deeply explore the adaptive molecular evolution of these genes. In this context, this work aimed to perform a more detailed analysis of the adaptive molecular evolution of SGPs in Anopheles, carrying out positive selection and gene families evolution analysis on 824 SGPs. Our results show that most SGPs have positively selected sites that can be used as targets in the development of new strategies for vector control. Notably, we were not able to find any evidence of an accelerated shift in the copy-number variation of SGPs compared with other proteins, as suggested in previous works.Significance StatementSalivary gland proteins (SGPs) are essential to blood-feeding behavior in Anopheles and they are the most studied class of proteins in blood-feeding insects. However a proper molecular evolution analysis on SGPs in Anopheles is missing. In our analyses we observed that most SGPs have positively selected sites and we were not able to find any evidence of an accelerated shift in the copy-number of SGPs compared with other proteins, as stated in the literature. Our results can open new venues in the development of new strategies for vector control.

scholarly journals Molecular evolution in large steps - Codon substitutions under positive selection

2019 ◽  
Author(s):  
Qingjian Chen ◽  
Ziwen He ◽  
Ao Lan ◽  
Haijun Wen ◽  
Chung-I Wu
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Negative Selection ◽  
Chemical Properties ◽  
Molecular Models ◽  
Step Size ◽  
Biochemical Basis ◽  
Mk Test ◽  
Physico Chemical ◽  
Adaptive Signal

AbstractMolecular evolution is believed to proceed in small steps. The step size can be defined by a distance reflecting physico-chemical disparities between amino acid (AA) pairs that can be exchanged by single 1 bp mutations. We show that AA substitution rates are strongly and negatively correlated with this distance but only when positive selection is relatively weak. We use the McDonald and Kreitman (MK) test to separate the influences of positive and negative selection. While negative selection is indeed stronger on AA substitutions generating larger changes in chemical properties of amino acids, positive selection operates by different rules. For 65 of the 75 possible pairs, positive selection is comparable in strength regardless of AA distance. However, the 10 pairs under the strongest positive selection all exhibit large leaps in chemical properties. Five of the 10 pairs are shared between hominoids andDrosophila, thus hinting at a common but modest biochemical basis of adaptation across taxa. The hypothesis that adaptive changes often take large functional steps will need to be extensively tested. If validated, molecular models will need to better integrate positive and negative selection in the search for adaptive signal.

scholarly journals Two decades of suspect evidence for adaptive molecular evolution - Negative selection confounding positive selection signals

2021 ◽  
Author(s):  
Qipian Chen ◽  
Hao Yang ◽  
Xiao Feng ◽  
Qingjian Chen ◽  
Suhua Shi ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Dna Sequences ◽  
Negative Selection ◽  
Genomic Sequence ◽  
Sequence Evolution ◽  
Mk Test ◽  
Random Expectation ◽  
Two Stages ◽  
Rule Out

There is a large literature in the last two decades affirming adaptive DNA sequences evolution between species. The main lines of evidence are from i) the McDonald-Kreitman (MK) test, which compares divergence and polymorphism data, and ii) the PAML test, which analyzes multi-species divergence data. Here, we apply these two tests concurrently on the genomic data of Drosophila and Arabidopsis. To our surprise, the >100 genes identified by the two tests do not overlap beyond random expectation. Because the non-concordance could be due to low powers leading to high false-negatives, we merge every 20 - 30 genes into a "supergene". At the supergene level, the power of detection is large but the calls still do not overlap. We rule out methodological reasons for the non-concordance. In particular, extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML, but not both. Since molecular evolution is governed by positive and negative selection concurrently, a fundamental assumption for estimating one (say, positive selection) is that the other is constant. However, in a broad survey of primates, birds, Drosophila and Arabidopsis, we found that negative selection rarely stays constant for long in evolution. As a consequence, the variation in negative selection is often mis-construed as signals of positive selection. In conclusion, MK, PAML or any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection. In a companion study, we propose a possible path forward in two stages – first, by mapping out the changes in negative selection and then using this map to estimate positive selection. For now, the large literature on positive selection between species has to await the re-assessment.

scholarly journals Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution

2019 ◽  
Vol 11 (10) ◽  
pp. 2702-2712 ◽  
Author(s):  
Qingjian Chen ◽  
Ao Lan ◽  
Xu Shen ◽  
Chung-I Wu
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Negative Selection ◽  
Evolutionary Rate ◽  
Small Step ◽  
Step Size ◽  
Entire Genome ◽  
Codon Substitution ◽  
Almost All ◽  
Codon Evolution

Abstract The widely accepted view that evolution proceeds in small steps is based on two premises: 1) negative selection acts strongly against large differences and 2) positive selection favors small-step changes. The two premises are not biologically connected and should be evaluated separately. We now extend a previous approach to studying codon evolution in the entire genome. Codon substitution rate is a function of the physicochemical distance between amino acids (AAs), equated with the step size of evolution. Between nine pairs of closely related species of plants, invertebrates, and vertebrates, the evolutionary rate is strongly and negatively correlated with a set of AA distances (ΔU, scaled to [0, 1]). ΔU, a composite measure of evolutionary rates across diverse taxa, is influenced by almost all of the 48 physicochemical properties used here. The new analyses reveal a crucial trend hidden from previous studies: ΔU is strongly correlated with the evolutionary rate (R2 > 0.8) only when the genes are predominantly under negative selection. Because most genes in most taxa are strongly constrained by negative selection, ΔU has indeed appeared to be a nearly universal measure of codon evolution. In conclusion, molecular evolution at the codon level generally takes small steps due to the prevailing negative selection. Whether positive selection may, or may not, follow the small-step rule is addressed in a companion study.

scholarly journals Molecular Evolution in Large Steps—Codon Substitutions under Positive Selection

2019 ◽  
Vol 36 (9) ◽  
pp. 1862-1873 ◽  
Author(s):  
Qingjian Chen ◽  
Ziwen He ◽  
Ao Lan ◽  
Xu Shen ◽  
Haijun Wen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Negative Selection ◽  
Chemical Properties ◽  
Molecular Models ◽  
Step Size ◽  
Biochemical Basis ◽  
Physico Chemical ◽  
Adaptive Signal

AbstractMolecular evolution is believed to proceed in small steps. The step size can be defined by a distance reflecting physico-chemical disparities between amino acid (AA) pairs that can be exchanged by single 1-bp mutations. We show that AA substitution rates are strongly and negatively correlated with this distance but only when positive selection is relatively weak. We use the McDonald and Kreitman test to separate the influences of positive and negative selection. While negative selection is indeed stronger on AA substitutions generating larger changes in chemical properties of AAs, positive selection operates by different rules. For 65 of the 75 possible pairs, positive selection is comparable in strength regardless of AA distance. However, the ten pairs under the strongest positive selection all exhibit large leaps in chemical properties. Five of the ten pairs are shared between Drosophila and Hominoids, thus hinting at a common but modest biochemical basis of adaptation across taxa. The hypothesis that adaptive changes often take large functional steps will need to be extensively tested. If validated, molecular models will need to better integrate positive and negative selection in the search for adaptive signal.

scholarly journals Isolation and characterization of a minor legumin and its constituent polypeptides from Pisum sativum (pea)

1988 ◽  
Vol 250 (3) ◽  
pp. 911-915 ◽  
Author(s):  
J F March ◽  
D J C Pappin ◽  
R Casey
Keyword(s):  
Pisum Sativum ◽  
Gene Families ◽  
Purification And Characterization ◽  
Isolation And Characterization ◽  
N Terminus ◽  
Electrophoretic Data ◽  
A Minor ◽  
First Time ◽  
Basic Polypeptides

The purification and characterization of a minor legumin species from Pisum sativum is described. Electrophoretic data indicate that it corresponds to a legumin subunit pair previously designated L1. The beta-polypeptides of the minor legumin have a phenylalanine N-terminus. This is the first time that an amino acid other than glycine has been reported as the N-terminus of the basic polypeptides from legumin-like proteins from any plant species. Sequence analyses of the isolated alpha- and beta-polypeptides of the minor legumin show that it does not correspond to any of the three legumin gene families that have previously been defined on the basis of DNA hybridizations and genetic analyses.

scholarly journals FUSTr: a tool to find gene families under selection in transcriptomes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4234 ◽  
Author(s):  
T. Jeffrey Cole ◽  
Michael S. Brewer
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
High Performance ◽  
Large Scale ◽  
Simulated Data ◽  
Gene Families ◽  
Strong Positive Selection ◽  
Transcriptomic Data ◽  
Downstream Analysis ◽  
User Friendly

Background The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. This is a tool that finds genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. Results When applied to previously studied spider transcriptomic data as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection in relatively little time. Conclusions FUSTr provides a useful tool for novice bioinformaticians to characterize the molecular evolution of organisms throughout the tree of life using large transcriptomic biodiversity datasets and can utilize multi-processor high-performance computational facilities.

TBE in Sweden

2020 ◽  
Keyword(s):  
Genetic Characterization ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Second Phase ◽  
Serum Samples ◽  
Tick Borne Encephalitis ◽  
Specific Immunoglobulin ◽  
Tick Borne Encephalitis Virus ◽  
First Time

Tick-borne encephalitis virus (TBEV) was isolated for the first time in Sweden in 1958 (from ticks and from 1 tick-borne encephalitis [TBE] patient).1 In 2003, Haglund and colleagues reported the isolation and antigenic and genetic characterization of 14 TBEV strains from Swedish patients (samples collected 1991–1994).2 The first serum sample, from which TBEV was isolated, was obtained 2–10 days after onset of disease and found to be negative for anti-TBEV immunoglobulin M (IgM) by enzyme-linked immunosorbent assay (ELISA), whereas TBEV-specific IgM (and TBEV-specific immunoglobulin G/cerebrospinal fluid [IgG/CSF] activity) was demonstrated in later serum samples taken during the second phase of the disease.

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