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1.
Microb Ecol ; 84(1): 267-284, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34436640

RESUMO

Bacteria are part of the insect gut system and influence many physiological traits of their host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis, endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterised. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into 6-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens.


Assuntos
Ceratopogonidae , Microbioma Gastrointestinal , Wolbachia , Animais , Insetos Vetores/microbiologia , RNA Ribossômico 16S/genética , Wolbachia/genética
2.
Microb Ecol ; 80(3): 703-717, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32462391

RESUMO

Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.


Assuntos
Aedes/virologia , Ceratopogonidae/virologia , Vírus Chikungunya/fisiologia , Microbioma Gastrointestinal/fisiologia , Insetos Vetores/virologia , Orthobunyavirus/fisiologia , Zika virus/fisiologia , Animais , Fenômenos Fisiológicos Bacterianos , Feminino , Mosquitos Vetores/virologia
3.
BMC Genomics ; 19(1): 798, 2018 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-30400848

RESUMO

BACKGROUND: Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads. RESULTS: Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. CONCLUSIONS: With Pacasus long-read technologies become available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.


Assuntos
Arabidopsis/genética , DNA/análise , Gorilla gorilla/genética , Nucleotídeos/genética , Análise de Sequência de DNA/métodos , Sequenciamento Completo do Genoma/métodos , Cromossomo Y/genética , Algoritmos , Animais , DNA/genética , Projetos de Pesquisa
4.
New Phytol ; 215(4): 1361-1369, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28737213

RESUMO

In contrast to mammals and vascular plants, microalgae show a high diversity in the N-glycan structures of complex N-glycoproteins. Although homologues for ß1,2-N-acetylglucosaminyltransferase I (GnTI), a key enzyme in the formation of complex N-glycans, have been identified in several algal species, GnTI-dependent N-glycans have not been detected so far. We have performed an N-glycoproteomic analysis of the hydrocarbon oils accumulating green microalgae Botryococcus braunii. Thereby, the analysis of intact N-glycopeptides allowed the determination of N-glycan compositions. Furthermore, insights into the role of N-glycosylation in B. braunii were gained from functional annotation of the identified N-glycoproteins. In total, 517 unique N-glycosylated peptides have been identified, including intact N-glycopeptides that harbored N-acetylhexosamine (HexNAc) at the nonreducing end. Surprisingly, these GnTI-dependent N-glycans were also found to be modified with (di)methylated hexose. The identification of GnTI-dependent N-glycans in combination with N-glycan methylation in B. braunii revealed an uncommon type of N-glycan processing in this microalgae.


Assuntos
Microalgas/enzimologia , N-Acetilglucosaminiltransferases/metabolismo , Polissacarídeos/metabolismo , Glicopeptídeos/metabolismo , Glicoproteínas/química , Glicoproteínas/metabolismo , Glicosilação , Metilação , Isótopos de Oxigênio , Polissacarídeos/química
5.
BMC Genomics ; 17: 670, 2016 08 23.
Artigo em Inglês | MEDLINE | ID: mdl-27552804

RESUMO

BACKGROUND: Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. RESULTS: Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. CONCLUSIONS: For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.


Assuntos
Cromossomos Fúngicos/genética , Fungos/genética , Análise de Sequência de DNA/métodos , Triticum/microbiologia , Composição de Bases , Elementos de DNA Transponíveis , Evolução Molecular , Duplicação Gênica , Tamanho do Genoma , Mutação Puntual , Reação em Cadeia da Polimerase em Tempo Real
6.
mSystems ; 6(3): e0111620, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34100635

RESUMO

Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype. IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.

7.
Commun Biol ; 4(1): 104, 2021 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-33483589

RESUMO

Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.


Assuntos
Evolução Biológica , Cromossomos de Insetos , Genoma de Inseto , Polydnaviridae/genética , Vespas/genética , Animais , Sequência de Bases , Sequência Conservada , Nudiviridae/genética , Receptores Odorantes/genética , Olfato , Simbiose , Sintenia , Vespas/virologia
8.
Microbiol Resour Announc ; 9(23)2020 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-32499356

RESUMO

The genomes of three Golubevia isolates (BC0812, BC0850, and BC0902) that have been shown to reduce conidiation of Blumeria graminis f. sp. tritici were sequenced using a dual-platform approach. The assembled genomes will help to elucidate the molecular mechanisms underlying the biocontrol effect of this understudied group.

9.
Sci Rep ; 9(1): 8672, 2019 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-31209237

RESUMO

Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.


Assuntos
Quitridiomicetos/genética , Proteínas Fúngicas/genética , Genoma Fúngico , Filogenia , Doenças das Plantas/microbiologia , Solanum tuberosum/microbiologia , Ascomicetos/classificação , Ascomicetos/genética , Ascomicetos/metabolismo , Basidiomycota/classificação , Basidiomycota/genética , Basidiomycota/metabolismo , Parede Celular/química , Parede Celular/microbiologia , Quitridiomicetos/classificação , Quitridiomicetos/metabolismo , Sequência Conservada , Proteínas Fúngicas/metabolismo , Duplicação Gênica , Expressão Gênica , Ontologia Genética , Variação Genética , Genômica/métodos , Guanina/metabolismo , Hidrolases/genética , Hidrolases/metabolismo , Repetições de Microssatélites , Anotação de Sequência Molecular , Células Vegetais/microbiologia , Mutação Puntual
10.
PLoS One ; 13(1): e0190279, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29293576

RESUMO

BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. RESULTS: The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. CONCLUSIONS: pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.


Assuntos
Alinhamento de Sequência/métodos , Algoritmos , Biologia Computacional , Computadores , Linguagens de Programação , Software
12.
PLoS One ; 10(4): e0122524, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25830241

RESUMO

MOTIVATION: To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. RESULTS: With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.


Assuntos
Alinhamento de Sequência , Análise de Sequência de DNA , Sequência de Bases , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Imunoglobulinas/genética , Polimorfismo de Nucleotídeo Único , Software
13.
BMC Res Notes ; 7: 34, 2014 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-24418292

RESUMO

BACKGROUND: Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. RESULTS: Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. CONCLUSION: The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.


Assuntos
Sequência de Bases , Biologia Computacional/métodos , Entropia , MicroRNAs/genética , Herpesvirus Humano 4/genética , Sequências Repetidas Invertidas , MicroRNAs/química , Dados de Sequência Molecular , Distribuição Normal , Conformação de Ácido Nucleico
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