scholarly journals De Novo Whole-Genome Assembly of the Swede Midge (Contarinia nasturtii), a Specialist of Brassicaceae, Using Linked-Read Sequencing

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Boyd A Mori ◽  
Cathy Coutu ◽  
Yolanda H Chen ◽  
Erin O Campbell ◽  
Julian R Dupuis ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Insect Pests ◽  
Management Strategies ◽  
Single Individual ◽  
Genes Encoding ◽  
Glutathione S Transferases ◽  
Swede Midge ◽  
Insect Interactions ◽  
Contarinia Nasturtii

Abstract The swede midge, Contarinia nasturtii, is a cecidomyiid fly that feeds specifically on plants within the Brassicaceae. Plants in this family employ a glucosinolate-myrosinase defense system, which can be highly toxic to nonspecialist feeders. Feeding by C. nasturtii larvae induces gall formation, which can cause substantial yield losses thus making it a significant agricultural pest. A lack of genomic resources, in particular a reference genome, has limited deciphering the mechanisms underlying glucosinolate tolerance in C. nasturtii, which is of particular importance for managing this species. Here, we present an annotated, scaffolded reference genome of C. nasturtii using linked-read sequencing from a single individual and explore systems involved in glucosinolate detoxification. The C. nasturtii genome is similar in size and annotation completeness to that of the Hessian fly, Mayetiola destructor, but has greater contiguity. Several genes encoding enzymes involved in glucosinolate detoxification in other insect pests, including myrosinases, sulfatases, and glutathione S-transferases, were found, suggesting that C. nasturtii has developed similar strategies for feeding on Brassicaceae. The C. nasturtii genome will, therefore, be integral to continued research on plant-insect interactions in this system and contribute to effective pest management strategies.

scholarly journals Identification and motif analyses of candidate nonreceptor olfactory genes of Dendroctonus adjunctus Blandford (Coleoptera: Curculionidae) from the head transcriptome

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Brenda Torres-Huerta ◽  
Obdulia L. Segura-León ◽  
Marco A. Aragón-Magadan ◽  
Héctor González-Hernández
Keyword(s):  
Bark Beetles ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Management Strategies ◽  
Beetle Species ◽  
Sequence Motifs ◽  
Homologous Proteins ◽  
Pine Beetle ◽  
Genes Encoding ◽  
Aggregation Behaviors

AbstractThe round-headed pine beetle Dendroctonus adjunctus, whose dispersion and colonization behaviors are linked to a communication system mediated by semiochemicals, is one of the five most critical primary pests in forest ecosystems in Mexico. This study provides the first head transcriptome analysis of D. adjunctus and the identification of the nonreceptor olfactory genes involved in the perception of odors. De novo assembly yielded 44,420 unigenes, and GO annotations were similar to those of antennal transcriptomes of other beetle species, which reflect metabolic processes related to smell and signal transduction. A total of 36 new transcripts of nonreceptor olfactory genes were identified, of which 27 encode OBPs, 7 encode CSPs, and 2 encode SNMP candidates, which were subsequently compared to homologous proteins from other bark beetles and Coleoptera species by searching for sequence motifs and performing phylogenetic analyses. Our study provides information on genes encoding nonreceptor proteins in D. adjunctus and broadens the knowledge of olfactory genes in Coleoptera and bark beetle species, and will help to understand colonization and aggregation behaviors for the development of tools that complement management strategies.

scholarly journals Insekticidni proteini in njihova uporaba za zatiranje koloradskega hrošča (Leptinotarsa decemlineata [Say, 1824])

2021 ◽  
Vol 117 (3) ◽  
pp. 1
Author(s):  
Primož ŽIGON ◽  
Jaka RAZINGER ◽  
Stanislav TRDAN
Keyword(s):  
Colorado Potato Beetle ◽  
Leptinotarsa Decemlineata ◽  
Insect Pests ◽  
Plant Protection ◽  
Management Strategies ◽  
Insecticidal Proteins ◽  
Potato Beetle ◽  
Genes Encoding ◽  
Leptinotarsa Decemlineata Say ◽  
Specific Proteins

<p class="042abstractstekst">Plants respond to pest attack, among other mechanisms, by producing specific proteins with insecticidal properties. Proteins with toxic effects on insects have also been discovered in many other organisms, especially fungi and bacteria. Due to their biological function, insecticidal proteins represent an important potential in the development of more environmentally friendly plant protection methods. Increasing knowledge about the mode of action of insecticidal proteins and the identification of genes encoding their synthesis enable the breeding of transgenic plants resistant to insect pests and the development of new bioinsecticidal agents. The Colorado potato beetle (<em>Leptinotarsa decemlineata</em>) is one of the most important pests of potato, so the study of such control methods is crucial for the development of sustainable integrated pest management strategies of potato. This review highlights the properties of some groups of insecticidal proteins and their modes of action, and summarizes examples of studies of their use for the control of Colorado potato beetle.</p>

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Cryo-EM structures of an insecticidal Bt toxin reveal its mechanism of action on the membrane

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Matthew J. Byrne ◽  
Matthew G. Iadanza ◽  
Marcos Arribas Perez ◽  
Daniel P. Maskell ◽  
Rachel M. George ◽  
...  
Keyword(s):  
Functional Data ◽  
Insect Pests ◽  
Economic Cost ◽  
Commercial Agriculture ◽  
Efficient Manner ◽  
Bt Toxin ◽  
Genes Encoding ◽  
Potential Applications ◽  
Chemical Pesticides ◽  
Wide Potential

AbstractInsect pests are a major cause of crop losses worldwide, with an estimated economic cost of $470 billion annually. Biotechnological tools have been introduced to control such insects without the need for chemical pesticides; for instance, the development of transgenic plants harbouring genes encoding insecticidal proteins. The Vip3 (vegetative insecticidal protein 3) family proteins from Bacillus thuringiensis convey toxicity to species within the Lepidoptera, and have wide potential applications in commercial agriculture. Vip3 proteins are proposed to exert their insecticidal activity through pore formation, though to date there is no mechanistic description of how this occurs on the membrane. Here we present cryo-EM structures of a Vip3 family toxin in both inactive and activated forms in conjunction with structural and functional data on toxin–membrane interactions. Together these data demonstrate that activated Vip3Bc1 complex is able to insert into membranes in a highly efficient manner, indicating that receptor binding is the likely driver of Vip3 specificity.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals Dravet syndrome associated mutations in GABRA1, GABRB2 and GABRG2 define the genetic landscape of defects of GABAA receptors

2021 ◽  
Author(s):  
Ciria C Hernandez ◽  
XiaoJuan Tian ◽  
Ningning Hu ◽  
Wangzhen Shen ◽  
Mackenzie A Catron ◽  
...  
Keyword(s):  
Gabaa Receptor ◽  
De Novo ◽  
Epileptic Encephalopathy ◽  
Dravet Syndrome ◽  
First Year ◽  
Genes Encoding ◽  
Genetic Landscape ◽  
Clonic Seizures ◽  
Trafficking Defects ◽  
First Year Of Life

Abstract Dravet syndrome is a rare, catastrophic epileptic encephalopathy that begins in the first year of life, usually with febrile or afebrile hemiclonic or generalized tonic-clonic seizures followed by status epilepticus. De novo variants in genes that mediate synaptic transmission such as SCN1A and PCDH19 are often associated with Dravet syndrome. Recently, GABAA receptor subunit genes (GABRs) encoding α1 (GABRA1), β3 (GABRB3) and γ2 (GABRG2), but not β2 (GABRB2) or β1 (GABRB1), subunits are frequently associated with Dravet syndrome or Dravet syndrome-like phenotype. We performed next generation sequencing on 870 patients with Dravet syndrome and identified nine variants in three different GABRs. Interestingly, the variants were all in genes encoding the most common GABAA receptor, the α1β2γ2 receptor. Mutations in GABRA1 (c.644T&gt;C, p.L215P; c.640C&gt;T, p.R214C; c.859G&gt;A; V287I; c.641G&gt;A, p.R214H) and GABRG2 (c.269C&gt;G, p.T90R; c.1025C&gt;T, p.P342L) presented as de novo cases, while in GABRB2 two variants were de novo (c.992T&gt;C, p.F331S; c.542A&gt;T, p.Y181F) and one was autosomal dominant and inherited from the maternal side (c.990_992del, p.330_331del). We characterized the effects of these GABR variants on GABAA receptor biogenesis and channel function. We found that defects in receptor gating were the common deficiency of GABRA1 and GABRB2 Dravet syndrome variants, while mainly trafficking defects were found with the GABRG2 (c.269C&gt;G, p.T90R) variant. It seems that variants in α1 and β2 subunits are less tolerated than in γ2 subunits, since variant α1 and β2 subunits express well but were functionally deficient. This suggests that all of these GABR variants are all targeting GABR genes that encode the assembled α1β2γ2 receptor, and regardless of which of the three subunits are mutated, variants in genes coding for α1, β2 and γ2 receptor subunits make them candidate causative genes in the pathogenesis of Dravet syndrome.

scholarly journals The Early Transcriptional Response of Human Granulocytes to Infection with Candida albicans Is Not Essential for Killing but Reflects Cellular Communications

2006 ◽  
Vol 75 (3) ◽  
pp. 1493-1501 ◽  
Author(s):  
Chantal Fradin ◽  
Abigail L. Mavor ◽  
Günther Weindl ◽  
Martin Schaller ◽  
Karin Hanke ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Mononuclear Cells ◽  
De Novo ◽  
Transcriptional Response ◽  
Mononuclear Leukocytes ◽  
General Notion ◽  
Genes Encoding ◽  
Global Transcriptional Profile ◽  
Life Threatening ◽  
Systemic Infections

ABSTRACT Candida albicans is a polymorphic opportunistic fungus that can cause life-threatening systemic infections following hematogenous dissemination in patients susceptible to nosocomial infection. Neutrophils form part of the innate immune response, which is the first line of defense against microbes and is particularly important in C. albicans infections. To compare the transcriptional response of leukocytes exposed to C. albicans, we investigated the expression of key cytokine genes in polymorphonuclear and mononuclear leukocytes after incubation with C. albicans for 1 h. Isolated mononuclear cells expressed high levels of genes encoding proinflammatory signaling molecules, whereas neutrophils exhibited much lower levels, similar to those observed in whole blood. The global transcriptional profile of neutrophils was examined by using an immunology-biased human microarray to determine whether different morphological forms or the viability of C. albicans altered the transcriptome. Hyphal cells appeared to have the broadest effect, although the most strongly induced genes were regulated independently of morphology or viability. These genes were involved in proinflammatory cell-cell signaling, cell signal transduction, and cell growth. Generally, genes encoding known components of neutrophil granules showed no upregulation at this time point; however, lactoferrin, a well-known candidacidal peptide, was secreted by neutrophils. Addition to inhibitors of RNA or protein de novo synthesis did not influence the killing activity within 30 min. These results support the general notion that neutrophils do not require gene transcription to mount an immediate and direct attack against microbes. However, neutrophils exposed to C. albicans express genes involved in communication with other immune cells.

Regulation of the SREBP transcription factors by mTORC1

2011 ◽  
Vol 39 (2) ◽  
pp. 495-499 ◽  
Author(s):  
Caroline A. Lewis ◽  
Beatrice Griffiths ◽  
Claudio R. Santos ◽  
Mario Pende ◽  
Almut Schulze
Keyword(s):  
Fatty Acid ◽  
Fatty Acid Synthase ◽  
Target Genes ◽  
De Novo ◽  
Regulatory Element ◽  
Cholesterol Biosynthesis ◽  
Mammalian Target Of Rapamycin ◽  
Lipid Biosynthesis ◽  
De Novo Lipogenesis ◽  
Genes Encoding

In recent years several reports have linked mTORC1 (mammalian target of rapamycin complex 1) to lipogenesis via the SREBPs (sterol-regulatory-element-binding proteins). SREBPs regulate the expression of genes encoding enzymes required for fatty acid and cholesterol biosynthesis. Lipid metabolism is perturbed in some diseases and SREBP target genes, such as FASN (fatty acid synthase), have been shown to be up-regulated in some cancers. We have previously shown that mTORC1 plays a role in SREBP activation and Akt/PKB (protein kinase B)-dependent de novo lipogenesis. Our findings suggest that mTORC1 plays a crucial role in the activation of SREBP and that the activation of lipid biosynthesis through the induction of SREBP could be part of a regulatory pathway that co-ordinates protein and lipid biosynthesis during cell growth. In the present paper, we discuss the increasing amount of data supporting the potential mechanisms of mTORC1-dependent activation of SREBP as well as the implications of this signalling pathway in cancer.

AStrap: identification of alternative splicing from transcript sequences without a reference genome

2018 ◽  
Vol 35 (15) ◽  
pp. 2654-2656 ◽  
Author(s):  
Guoli Ji ◽  
Wenbin Ye ◽  
Yaru Su ◽  
Moliang Chen ◽  
Guangzao Huang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Alternative Splicing ◽  
Single Molecule ◽  
Reference Genome ◽  
De Novo ◽  
Supplementary Information ◽  
Model Organisms ◽  
Sequencing Data ◽  
Extensive Evaluation ◽  
Reference Genomes

Abstract Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources. Availability and implementation AStrap is available for download at https://github.com/BMILAB/AStrap. Supplementary information Supplementary data are available at Bioinformatics online.

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