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1.
Int J Parasitol ; 54(2): 89-98, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37652224

RESUMO

The heartworm, Dirofilaria immitis, is a filarial parasitic nematode responsible for significant morbidity and mortality in wild and domesticated canids. Resistance to macrocyclic lactone drug prevention represents a significant threat to parasite control and has prompted investigations to understand the genetic determinants of resistance. This study aimed to improve the genomic resources of D. immitis to enable a more precise understanding of how genetic variation is distributed within and between parasite populations worldwide, which will inform the likelihood and rate by which parasites, and in turn, resistant alleles, might spread. We have guided the scaffolding of a recently published genome assembly for D. immitis (ICBAS_JMDir_1.0) using the chromosomal-scale reference genomes of Brugia malayi and Onchocerca volvulus, resulting in an 89.5 Mb assembly composed of four autosomal- and one sex-linked chromosomal-scale scaffolds representing 99.7% of the genome. Publicly available and new whole-genome sequencing data from 32 D. immitis samples from Australia, Italy and the USA were assessed using principal component analysis, nucleotide diversity (Pi) and absolute genetic divergence (Dxy) to characterise the global genetic structure and measure within- and between-population diversity. These population genetic analyses revealed broad-scale genetic structure among globally diverse samples and differences in genetic diversity between populations; however, fine-scale subpopulation analysis was limited and biased by differences between sample types. Finally, we mapped single nucleotide polymorphisms previously associated with macrocyclic lactone resistance in the new genome assembly, revealing the physical linkage of high-priority variants on chromosome 3, and determined their frequency in the studied populations. This new chromosomal assembly for D. immitis now allows for a more precise investigation of selection on genome-wide genetic variation and will enhance our understanding of parasite transmission and the spread of genetic variants responsible for resistance to treatment.


Assuntos
Dirofilaria immitis , Dirofilariose , Doenças do Cão , Cães , Animais , Dirofilaria immitis/genética , Metagenômica , Genoma Helmíntico , Lactonas , Austrália , Dirofilariose/epidemiologia , Doenças do Cão/parasitologia
2.
Mol Biol Evol ; 40(12)2023 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-37979163

RESUMO

Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of 2 homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species is accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of 2 sublines of the commonly used inbred line of M. lignano (called DV1) differing only in a copy number of the largest chromosome (MLI1). Using nontrivial assembly free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists of (i) presence of 3 subgenomes, which emerged via formation of large fused chromosomes and its variants, and (ii) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.


Assuntos
Platelmintos , Animais , Platelmintos/genética , Cromossomos/genética , Genoma Helmíntico , Poliploidia , Sequência de Bases
3.
PLoS Genet ; 19(7): e1010832, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37399201

RESUMO

Adaptation of organisms to environmental change may be facilitated by the creation of new genes. New genes without homologs in other lineages are known as taxonomically-restricted orphan genes and may result from divergence or de novo formation. Previously, we have extensively characterized the evolution and origin of such orphan genes in the nematode model organism Pristionchus pacificus. Here, we employ large-scale transcriptomics to establish potential functional associations and to measure the degree of transcriptional plasticity among orphan genes. Specifically, we analyzed 24 RNA-seq samples from adult P. pacificus worms raised on 24 different monoxenic bacterial cultures. Based on coexpression analysis, we identified 28 large modules that harbor 3,727 diplogastrid-specific orphan genes and that respond dynamically to different bacteria. These coexpression modules have distinct regulatory architecture and also exhibit differential expression patterns across development suggesting a link between bacterial response networks and development. Phylostratigraphy revealed a considerably high number of family- and even species-specific orphan genes in certain coexpression modules. This suggests that new genes are not attached randomly to existing cellular networks and that integration can happen very fast. Integrative analysis of protein domains, gene expression and ortholog data facilitated the assignments of biological labels for 22 coexpression modules with one of the largest, fast-evolving module being associated with spermatogenesis. In summary, this work presents the first functional annotation for thousands of P. pacificus orphan genes and reveals insights into their integration into environmentally responsive gene networks.


Assuntos
Genoma Helmíntico , Nematoides , Animais , Nematoides/genética , Nematoides/microbiologia
4.
Int J Mol Sci ; 24(14)2023 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-37511167

RESUMO

Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes-a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species-Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the 'blind spots' of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes.


Assuntos
DNA Mitocondrial , Genoma Helmíntico , Genoma Mitocondrial , Helmintos , Sequências Repetidas Invertidas , DNA Mitocondrial/química , DNA Mitocondrial/genética , Helmintos/classificação , Helmintos/genética , Helmintos/ultraestrutura , Animais , Filogenia , Masculino , Feminino , Conformação de Ácido Nucleico
5.
Sci Data ; 10(1): 317, 2023 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-37231051

RESUMO

Sipuncula is a class of exocoelomic unsegmented animals whose evolutionary relationships are unresolved. The peanut worm Sipunculus nudus is a globally distributed, economically important species belonging to the class Sipuncula. Herein, we present the first high-quality chromosome-level assembly of S. nudus based on HiFi reads and high-resolution chromosome conformation capture (Hi-C) data. The assembled genome was 1,427 Mb, with a contig N50 length of 29.46 Mb and scaffold N50 length of 80.87 Mb. Approximately 97.91% of the genome sequence was anchored to 17 chromosomes. A BUSCO assessment showed that 97.7% of the expectedly conserved genes were present in the genome assembly. The genome was composed of 47.91% repetitive sequences, and 28,749 protein-coding genes were predicted. A phylogenetic tree demonstrated that Sipuncula belongs to Annelida and diverged from the common ancestor of Polychaeta. The high-quality chromosome-level genome of S. nudus will serve as a valuable reference for studies of the genetic diversity and evolution of Lophotrochozoa.


Assuntos
Genoma Helmíntico , Nematoides , Animais , Cromossomos/genética , Filogenia , Sequências Repetitivas de Ácido Nucleico
6.
Trends Parasitol ; 38(10): 831-840, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35810065

RESUMO

Rapid advancement in high-throughput sequencing and analytical approaches has seen a steady increase in the generation of genomic resources for helminth parasites. Now, helminth genomes and their annotations are a cornerstone of numerous efforts to compare genetic and transcriptomic variation, from single cells to populations of globally distributed parasites, to genome modifications to understand gene function. Our understanding of helminths is increasingly reliant on these genomic resources, which are primarily static once published and vary widely in quality and completeness between species. This article seeks to highlight the cause and effect of this variation and argues for the continued improvement of these genomic resources - even after their publication - which is necessary to provide a more accurate and complete understanding of the biology of these important pathogens.


Assuntos
Helmintos , Parasitos , Animais , Genoma , Genoma Helmíntico/genética , Genômica , Helmintos/genética , Parasitos/genética
7.
Methods Mol Biol ; 2468: 215-237, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35320567

RESUMO

The clustered, regularly interspaced, short, palindromic repeat (CRISPR)-associated (CAS) nuclease Cas9 has been used in many organisms to generate specific mutations and transgene insertions. Here we describe our most up-to-date protocols using the S. pyogenes Cas9 in C. elegans that provides a convenient and effective approach for making heritable changes to the worm genome. We present several considerations when deciding which strategy best suits the needs of the experiment.


Assuntos
Sistemas CRISPR-Cas , Caenorhabditis elegans , Edição de Genes , Genoma Helmíntico , Animais , Proteína 9 Associada à CRISPR , Caenorhabditis elegans/genética , Edição de Genes/métodos
8.
Mar Drugs ; 20(2)2022 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-35200659

RESUMO

Due to their high biodiversity and adaptation to a mutable and challenging environment, aquatic lophotrochozoan animals are regarded as a virtually unlimited source of bioactive molecules. Among these, lectins, i.e., proteins with remarkable carbohydrate-recognition properties involved in immunity, reproduction, self/nonself recognition and several other biological processes, are particularly attractive targets for biotechnological research. To date, lectin research in the Lophotrochozoa has been restricted to the most widespread phyla, which are the usual targets of comparative immunology studies, such as Mollusca and Annelida. Here we provide the first overview of the repertoire of the secretory lectin-like molecules encoded by the genomes of six target rotifer species: Brachionus calyciflorus, Brachionus plicatilis, Proales similis (class Monogononta), Adineta ricciae, Didymodactylos carnosus and Rotaria sordida (class Bdelloidea). Overall, while rotifer secretory lectins display a high molecular diversity and belong to nine different structural classes, their total number is significantly lower than for other groups of lophotrochozoans, with no evidence of lineage-specific expansion events. Considering the high evolutionary divergence between rotifers and the other major sister phyla, their widespread distribution in aquatic environments and the ease of their collection and rearing in laboratory conditions, these organisms may represent interesting targets for glycobiological studies, which may allow the identification of novel carbohydrate-binding proteins with peculiar biological properties.


Assuntos
Organismos Aquáticos , Lectinas/metabolismo , Rotíferos/metabolismo , Animais , Genoma Helmíntico
9.
Pest Manag Sci ; 78(3): 1213-1226, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-34839581

RESUMO

BACKGROUND: Bursaphelenchus xylophilus, the pinewood nematode, kills millions of pine trees worldwide every year, and causes enormous economic and ecological losses. Despite extensive research on population variation, there is little understanding of the population-wide variation spectrum in China. RESULTS: We sequenced an inbred B. xylophilus strain using Pacbio+Illumina+Bionano+Hi-C and generated a chromosome-level assembly (AH1) with six chromosomes of 77.1 Mb (chromosome N50: 12 Mb). The AH1 assembly shows very high continuity and completeness, and contains novel genes with potentially important functions compared with previous assemblies. Subsequently, we sequenced 181 strains from China and the USA and found ~7.8 million single nucleotide polymorphisms (SNPs). Analysis shows that the B. xylophilus population in China can be divided into geographically bounded subpopulations with severe cross-infection and potential migrations. In addition, distribution of B. xylophilus is dominated by temperature zones while geographically associated SNPs are mainly located on adaptation related GPCR gene families, suggesting the nematode has been evolving to adapt to different temperatures. A machine-learning based epidemic tracking method has been established to predict their geographical origins, which can be applied to any other species. CONCLUSION: Our study provides the community with the first high-quality chromosome-level assembly which includes a comprehensive catalogue of genetic variations. It provides insights into population structure and effective tracking method for this invasive species, which facilitates future studies to address a variety of applied, genomic and evolutionary questions in B. xylophilus as well as related species.


Assuntos
Genética Populacional , Pinus , Rabditídios , Animais , China , Cromossomos , Genoma Helmíntico , Pinus/parasitologia , Rabditídios/genética , Sequenciamento Completo do Genoma
10.
PLoS Negl Trop Dis ; 15(12): e0010062, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34941866

RESUMO

Schistosomes cause schistosomiasis, the world's second most important parasitic disease after malaria in terms of public health and social-economic impacts. A peculiar feature of these dioecious parasites is their ability to produce viable and fertile hybrid offspring. Originally only present in the tropics, schistosomiasis is now also endemic in southern Europe. Based on the analysis of two genetic markers the European schistosomes had previously been identified as hybrids between the livestock- and the human-infective species Schistosoma bovis and Schistosoma haematobium, respectively. Here, using PacBio long-read sequencing technology we performed genome assembly improvement and annotation of S. bovis, one of the parental species for which no satisfactory genome assembly was available. We then describe the whole genome introgression levels of the hybrid schistosomes, their morphometric parameters (eggs and adult worms) and their compatibility with two European snail strains used as vectors (Bulinus truncatus and Planorbarius metidjensis). Schistosome-snail compatibility is a key parameter for the parasites life cycle progression, and thus the capability of the parasite to establish in a given area. Our results show that this Schistosoma hybrid is strongly introgressed genetically, composed of 77% S. haematobium and 23% S. bovis origin. This genomic admixture suggests an ancient hybridization event and subsequent backcrosses with the human-specific species, S. haematobium, before its introduction in Corsica. We also show that egg morphology (commonly used as a species diagnostic) does not allow for accurate hybrid identification while genetic tests do.


Assuntos
Genoma Helmíntico , Hibridização Genética , Schistosoma haematobium/crescimento & desenvolvimento , Schistosoma haematobium/genética , Schistosoma/crescimento & desenvolvimento , Schistosoma/genética , Animais , Tamanho Corporal , Bulinus/parasitologia , Quimera/anatomia & histologia , Quimera/genética , Quimera/crescimento & desenvolvimento , Vetores de Doenças , Europa (Continente) , Feminino , Humanos , Masculino , Schistosoma/anatomia & histologia , Schistosoma haematobium/anatomia & histologia , Esquistossomose/parasitologia , Caramujos/parasitologia
11.
PLoS Genet ; 17(11): e1009755, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34748534

RESUMO

Gene editing in C. elegans using plasmid-based CRISPR reagents requires microinjection of many animals to produce a single edit. Germline silencing of plasmid-borne Cas9 is a major cause of inefficient editing. Here, we present a set of C. elegans strains that constitutively express Cas9 in the germline from an integrated transgene. These strains markedly improve the success rate for plasmid-based CRISPR edits. For simple, short homology arm GFP insertions, 50-100% of injected animals typically produce edited progeny, depending on the target locus. Template-guided editing from an extrachromosomal array is maintained over multiple generations. We have built strains with the Cas9 transgene on multiple chromosomes. Additionally, each Cas9 locus also contains a heatshock-driven Cre recombinase for selectable marker removal and a bright fluorescence marker for easy outcrossing. These integrated Cas9 strains greatly reduce the workload for producing individual genome edits.


Assuntos
Proteína 9 Associada à CRISPR/genética , Sistemas CRISPR-Cas , Caenorhabditis elegans/genética , Edição de Genes/métodos , Genoma Helmíntico , Animais
12.
Int J Mol Sci ; 22(22)2021 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-34830338

RESUMO

Insulin/IGF-1-like signaling (IIS) plays a crucial, conserved role in development, growth, reproduction, stress tolerance, and longevity. In Caenorhabditis elegans, the enhanced longevity under reduced insulin signaling (rIIS) is primarily regulated by the transcription factors (TFs) DAF-16/FOXO, SKN-1/Nrf-1, and HSF1/HSF-1. The specific and coordinated regulation of gene expression by these TFs under rIIS has not been comprehensively elucidated. Here, using RNA-sequencing analysis, we report a systematic study of the complexity of TF-dependent target gene interactions during rIIS under analogous genetic and experimental conditions. We found that DAF-16 regulates only a fraction of the C. elegans transcriptome but controls a large set of genes under rIIS; SKN-1 and HSF-1 show the opposite trend. Both of the latter TFs function as activators and repressors to a similar extent, while DAF-16 is predominantly an activator. For expression of the genes commonly regulated by TFs under rIIS conditions, DAF-16 is the principal determining factor, dominating over the other two TFs, irrespective of whether they activate or repress these genes. The functional annotations and regulatory networks presented in this study provide novel insights into the complexity of the gene regulatory networks downstream of the IIS pathway that controls diverse phenotypes, including longevity.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Proteínas de Ligação a DNA/genética , Fatores de Transcrição Forkhead/genética , Genoma Helmíntico , Insulina/metabolismo , Fatores de Transcrição/genética , Transcriptoma , Animais , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Ligação a DNA/metabolismo , Fatores de Transcrição Forkhead/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Ontologia Genética , Redes Reguladoras de Genes , Longevidade/genética , Anotação de Sequência Molecular , Fenótipo , Transdução de Sinais , Fatores de Transcrição/metabolismo
13.
Parasit Vectors ; 14(1): 574, 2021 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-34772444

RESUMO

BACKGROUND: The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. METHODS: Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. RESULTS: At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. CONCLUSIONS: The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments.


Assuntos
Processamento Alternativo , Echinococcus granulosus/crescimento & desenvolvimento , Echinococcus granulosus/genética , Genoma Helmíntico , Proteínas de Helminto/genética , Spliceossomos/genética , Animais , Echinococcus granulosus/metabolismo , Perfilação da Expressão Gênica , Proteínas de Helminto/metabolismo , Estágios do Ciclo de Vida , Spliceossomos/metabolismo , Transcriptoma
14.
PLoS Negl Trop Dis ; 15(10): e0009838, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34705823

RESUMO

The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping in order to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (πX/πA = 0.2), which is lower than the expected (πX/πA = 0.75). A reduction in diversity is also observed in other filarial nematodes with neo-X chromosome fusions in the genera Onchocerca and Wuchereria, but not those without neo-X chromosome fusions in the genera Loa and Dirofilaria. In the species with neo-X chromosome fusions, chromosome X is abnormally large, containing a third of the genetic material such that a sizable portion of the genome is lacking sequence diversity. Such profound differences in genetic diversity can be consequential, having been associated with drug resistance and adaptability, with the potential to affect filarial eradication.


Assuntos
Brugia/genética , Variação Genética , Cromossomo X/genética , Animais , Brugia/classificação , Aberrações Cromossômicas , Genoma Helmíntico
15.
PLoS One ; 16(10): e0258269, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34614038

RESUMO

Ionizing radiation (IR) is widely used in cancer therapy and accidental or environmental exposure is a major concern. However, little is known about the genome-wide effects IR exerts on germ cells and the relative contribution of DNA repair pathways for mending IR-induced lesions. Here, using C. elegans as a model system and using primary sequencing data from our recent high-level overview of the mutagenic consequences of 11 genotoxic agents, we investigate in detail the genome-wide mutagenic consequences of exposing wild-type and 43 DNA repair and damage response defective C. elegans strains to a Caesium (Cs-137) source, emitting γ-rays. Cs-137 radiation induced single nucleotide variants (SNVs) at a rate of ~1 base substitution per 3 Gy, affecting all nucleotides equally. In nucleotide excision repair mutants, this frequency increased 2-fold concurrently with increased dinucleotide substitutions. As observed for DNA damage induced by bulky DNA adducts, small deletions were increased in translesion polymerase mutants, while base changes decreased. Structural variants (SVs) were augmented with dose, but did not arise with significantly higher frequency in any DNA repair mutants tested. Moreover, 6% of all mutations occurred in clusters, but clustering was not significantly altered in any DNA repair mutant background. Our data is relevant for better understanding how DNA repair pathways modulate IR-induced lesions.


Assuntos
Caenorhabditis elegans/genética , Caenorhabditis elegans/efeitos da radiação , Reparo do DNA/genética , Reparo do DNA/efeitos da radiação , Genoma Helmíntico , Radiação Ionizante , Animais , Caenorhabditis elegans/efeitos dos fármacos , Cisplatino/farmacologia , Reparo do DNA/efeitos dos fármacos , Humanos , Mutação/genética , Neoplasias/genética , Polimorfismo de Nucleotídeo Único/genética , Raios Ultravioleta
16.
PLoS Negl Trop Dis ; 15(10): e0009750, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34610021

RESUMO

Fasciola gigantica and Fasciola hepatica are causative pathogens of fascioliasis, with the widest latitudinal, longitudinal, and altitudinal distribution; however, among parasites, they have the largest sequenced genomes, hindering genomic research. In the present study, we used various sequencing and assembly technologies to generate a new high-quality Fasciola gigantica reference genome. We improved the integration of gene structure prediction, and identified two independent transposable element expansion events contributing to (1) the speciation between Fasciola and Fasciolopsis during the Cretaceous-Paleogene boundary mass extinction, and (2) the habitat switch to the liver during the Paleocene-Eocene Thermal Maximum, accompanied by gene length increment. Long interspersed element (LINE) duplication contributed to the second transposon-mediated alteration, showing an obvious trend of insertion into gene regions, regardless of strong purifying effect. Gene ontology analysis of genes with long LINE insertions identified membrane-associated and vesicle secretion process proteins, further implicating the functional alteration of the gene network. We identified 852 predicted excretory/secretory proteins and 3300 protein-protein interactions between Fasciola gigantica and its host. Among them, copper/zinc superoxide dismutase genes, with specific gene copy number variations, might play a central role in the phase I detoxification process. Analysis of 559 single-copy orthologs suggested that Fasciola gigantica and Fasciola hepatica diverged at 11.8 Ma near the Middle and Late Miocene Epoch boundary. We identified 98 rapidly evolving gene families, including actin and aquaporin, which might explain the large body size and the parasitic adaptive character resulting in these liver flukes becoming epidemic in tropical and subtropical regions.


Assuntos
Doenças dos Bovinos/parasitologia , Elementos de DNA Transponíveis , Evolução Molecular , Fasciola/genética , Fasciolíase/veterinária , Genoma Helmíntico , Adaptação Fisiológica , Animais , Búfalos/parasitologia , Bovinos , Fasciola/classificação , Fasciola/fisiologia , Fasciolíase/parasitologia , Fasciolíase/fisiopatologia , Genômica , Proteínas de Helminto/genética , Interações Hospedeiro-Parasita , Filogenia
17.
Parasit Vectors ; 14(1): 537, 2021 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-34649597

RESUMO

BACKGROUND: Necator americanus is one of the major etiological agents of human ancylostomiasis. Historically, the epidemiology of ancylostomiasis in Henan Province of central China and the molecular characteristics of N. americanus have been poorly understood. METHODS: In this study, we report a case of ancylostomiasis in Zhengzhou city of Henan Province. We also review the epidemiology of ancylostomiasis in Henan Province from 1949 to 2020. In addition, the complete mitochondrial (mt) genome of one clinical isolate is fully characterized using Illumina sequencing. All available mt genomes of hookworms in GenBank were included to reconstruct the phylogeny using both maximum likelihood (ML) and Bayesian inference (BI) methods. RESULTS: A total of three worms were collected from the patient. These worms were identified as N. americanus based on morphological characteristics as well as confirmed by genotyping with the barcoding gene cox1. Although ancylostomiasis cases have dropped substantially in recent years, hookworm infection is still a public health problem in underdeveloped areas and remote rural areas in Henan Province. The mt genome features of the N. americanus contained 12 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a major non-coding region. The nad1 gene showed high sequence variability among isolates, which is worth considering for future genetic studies of N. americanus. Phylogenetic analyses support the monophyly of hookworm isolates from different hosts and distinct geographical locations. CONCLUSIONS: The mt genome of N. americanus presented here will serve as a useful data set for studying population genetics and phylogenetic relationships of hookworms. Positive measures for preventing and controlling ancylostomiasis are required by both health services and individuals in Henan Province.


Assuntos
Ancilostomíase/epidemiologia , Genoma Helmíntico , Técnicas de Diagnóstico Molecular , Necator americanus/genética , Necatoríase/diagnóstico , Necatoríase/epidemiologia , Idoso , Animais , China/epidemiologia , DNA de Helmintos/genética , Feminino , Humanos , Necator americanus/isolamento & purificação
18.
Nucleic Acids Res ; 49(18): 10573-10588, 2021 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-34551436

RESUMO

The twister ribozyme is widely distributed over numerous organisms and is especially abundant in Schistosoma mansoni, but has no confirmed biological function. Of the 17 non-LTR retrotransposons known in S. mansoni, none have thus far been associated with ribozymes. Here we report the identification of novel twister variant (T-variant) ribozymes and their function in S. mansoni non-LTR retrotransposition. We show that T-variant ribozymes are located at the 5' end of Perere-3 non-LTR retrotransposons in the S. mansoni genome. T-variant ribozymes were demonstrated to be catalytically active in vitro. In reporter constructs, T-variants were shown to cleave in vivo, and cleavage of T-variants was sufficient for the translation of downstream reporter genes. Our analysis shows that the T-variants and Perere-3 are transcribed together. Target site duplications (TSDs); markers of target-primed reverse transcription (TPRT) and footmarks of retrotransposition, are located adjacent to the T-variant cleavage site and suggest that T-variant cleavage has taken place inS. mansoni. Sequence heterogeneity in the TSDs indicates that Perere-3 retrotransposition is not site-specific. The TSD sequences contribute to the 5' end of the terminal ribozyme helix (P1 stem). Based on these results we conclude that T-variants have a functional role in Perere-3 retrotransposition.


Assuntos
RNA Catalítico/química , Retroelementos , Schistosoma mansoni/genética , Animais , Sequência de Bases , Genoma Helmíntico , RNA Catalítico/metabolismo , Schistosoma mansoni/enzimologia
19.
Nucleic Acids Res ; 49(19): 11167-11180, 2021 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-34586415

RESUMO

microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Proteínas de Ciclo Celular/genética , Genoma Helmíntico , MicroRNAs/genética , RNA de Helmintos/genética , Uridina Monofosfato/metabolismo , Monofosfato de Adenosina/metabolismo , Animais , Caenorhabditis elegans/classificação , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Ciclo Celular/metabolismo , Galinhas/classificação , Galinhas/genética , Galinhas/metabolismo , Sequência Conservada , Regulação da Expressão Gênica , Meia-Vida , Humanos , Camundongos , MicroRNAs/antagonistas & inibidores , MicroRNAs/classificação , MicroRNAs/metabolismo , Filogenia , Interferência de RNA , Estabilidade de RNA , RNA de Helmintos/classificação , RNA de Helmintos/metabolismo , Especificidade da Espécie , Peixe-Zebra/classificação , Peixe-Zebra/genética , Peixe-Zebra/metabolismo
20.
Sci Rep ; 11(1): 18258, 2021 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-34521941

RESUMO

Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.


Assuntos
Caenorhabditis elegans/genética , Rearranjo Gênico/genética , Sequenciamento Completo do Genoma/métodos , Animais , Troca Genética/genética , Variações do Número de Cópias de DNA/genética , Duplicação Gênica/genética , Genoma Helmíntico/genética , Heterozigoto , Homozigoto , Mutagênese/genética
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