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1.
Parasitol Res ; 118(12): 3195-3204, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31724068

RESUMO

Whole genomic sequencing (WGS) and comparative genomics are increasingly used in the characterization of Cryptosporidium spp. They are facilitated by the establishment of procedures for WGS analysis of clinical specimens without laboratory propagation of pathogens. Results of recent comparative genomics analysis suggest that gene duplication might be associated with broad host ranges of some zoonotic Cryptosporidium species and subtypes, while genetic recombination could be involved in the emergence of virulent subtypes. The availability of WGS data has further facilitated the development of advanced molecular typing tools. The use of these tools together with comparative genomics analyses has begun to improve the investigations of outbreaks in industrialized nations. More WGS data, however, are needed from both industrialized nations and developing countries before we can have in-depth understanding of the population genetics and evolution of Cryptosporidium spp. and genetic determinants of various phenotypic traits in human-pathogenic subtypes.


Assuntos
Criptosporidiose/epidemiologia , Cryptosporidium/genética , Genômica , Animais , Criptosporidiose/parasitologia , Criptosporidiose/transmissão , Cryptosporidium/classificação , Cryptosporidium/patogenicidade , Genoma de Protozoário/genética , Genótipo , Especificidade de Hospedeiro/genética , Humanos , Epidemiologia Molecular , Virulência/genética
2.
BMC Genomics ; 20(1): 744, 2019 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-31619176

RESUMO

BACKGROUND: Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Alberta, Canada in 2003. Genetic resistance to clubroot in an adapted canola cultivar has been available since 2009, but resistance breakdown was detected in 2013 and new pathotypes are increasing rapidly. Information on genetic similarity among pathogen populations across Canada could be useful in estimating the genetic variation in pathogen populations, predicting the effect of subsequent selection pressure on changes in the pathogen population over time, and even in identifying the origin of the initial pathogen introduction to canola in Alberta. RESULTS: The genomic sequences of 43 strains (34 field collections, 9 single-spore isolates) of P. brassicae from Canada, the United States, and China clustered into five clades based on SNP similarity. The strains from Canada separated into four clades, with two containing mostly strains from the Prairies (provinces of Alberta, Saskatchewan, and Manitoba) and two that were mostly from the rest of Canada or the USA. Several strains from China formed a separate clade. More than one pathotype and host were present in all four Canadian clades. The initial pathotypes from canola on the Prairies clustered separately from the pathotypes on canola that could overcome resistance to the initial pathotypes. Similarly, at one site in central Canada where resistance had broken down, about half of the genes differed (based on SNPs) between strains before and after the breakdown. CONCLUSION: Clustering based on genome-wide DNA sequencing demonstrated that the initial pathotypes on canola on the Prairies clustered separately from the new virulent pathotypes on the Prairies. Analysis indicated that these 'new' pathotypes were likely present in the pathogen population at very low frequency, maintained through balancing selection, and increased rapidly in response to selection from repeated exposure to host resistance.


Assuntos
Brassica napus/parasitologia , Genoma de Protozoário/genética , Plasmodioforídeos/genética , Plasmodioforídeos/patogenicidade , Canadá , China , DNA de Protozoário/genética , Resistência à Doença , Variação Genética , Genética Populacional , Filogenia , Doenças das Plantas/parasitologia , Plasmodioforídeos/classificação , Seleção Genética , Análise de Sequência de DNA , Estados Unidos
3.
Nucleic Acids Res ; 47(18): 9741-9760, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31504770

RESUMO

Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.


Assuntos
DNA Circular/genética , Rearranjo Gênico/genética , Oxytricha/genética , Recombinação Genética , Citoplasma/genética , Elementos de DNA Transponíveis/genética , DNA de Protozoário/genética , Células Eucarióticas , Genoma de Protozoário/genética , Sequenciamento de Nucleotídeos em Larga Escala
4.
Mem Inst Oswaldo Cruz ; 114: e190147, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31553371

RESUMO

BACKGROUND: Calpains are proteins belonging to the multi-gene family of calcium-dependent cysteine peptidases that undergo tight on/off regulation, and uncontrolled proteolysis of calpains is associated with severe human pathologies. Calpain orthologues are expanded and diversified in the trypanosomatids genome. OBJECTIVES: Here, we characterised calpains in Leishmania braziliensis, the main causative agent of cutaneous leishmaniasis in Brazil. METHODS/FINDINGS: In total, 34 predicted calpain-like genes were identified. After domain structure evaluation, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) during in vitro metacyclogenesis revealed (i) five genes with enhanced expression in the procyclic stage, (ii) one augmented gene in the metacyclic stage, and (iii) one procyclic-exclusive transcript. Western blot analysis revealed that an antibody against a consensus-conserved peptide reacted with multiple calpain-like proteins, which is consistent with the multi-gene family characteristic. Flow cytometry and immunocytochemistry analyses revealed the presence of calpain-like molecules mainly in the cytoplasm, to a lesser extent in the plasma membrane, and negligible levels in the nucleus, which are all consistent with calpain localisation. Eventually, the calpain inhibitor MDL28170 was used for functional studies revealing (i) a leishmaniostatic effect, (ii) a reduction in the association index in mouse macrophages, (iii) ultra-structural alterations conceivable with autophagy, and (iv) an enhanced expression of the virulence factor GP63. CONCLUSION: This report adds novel insights into the domain structure, expression, and localisation of L. braziliensis calpain-like molecules.


Assuntos
Calpaína/genética , Genoma de Protozoário/genética , Leishmania braziliensis/química , Macrófagos Peritoneais/metabolismo , Animais , Western Blotting , Calpaína/efeitos dos fármacos , Calpaína/metabolismo , Calpaína/ultraestrutura , Inibidores de Cisteína Proteinase/farmacologia , Dipeptídeos/farmacologia , Citometria de Fluxo , Regulação da Expressão Gênica , Imuno-Histoquímica , Leishmania braziliensis/genética , Leishmania braziliensis/metabolismo , Leishmania braziliensis/ultraestrutura , Camundongos , Camundongos Endogâmicos BALB C , Microscopia Eletrônica de Transmissão , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Virulência
5.
Mol Plant Microbe Interact ; 32(12): 1559-1563, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31479390

RESUMO

Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N50 of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N50 length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.


Assuntos
Genoma de Protozoário , Phytophthora , Análise de Sequência de DNA , Tamanho do Genoma , Genoma de Protozoário/genética , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Phytophthora/genética
6.
Protist ; 170(4): 358-373, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31415953

RESUMO

The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.


Assuntos
Dinoflagelados/classificação , Dinoflagelados/genética , Genoma de Protozoário/genética , Plastídeos/genética , Transcriptoma/genética , Perfilação da Expressão Gênica , Genômica
7.
Clin Microbiol Rev ; 32(4)2019 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-31366610

RESUMO

Protozoan Plasmodium parasites are the causative agents of malaria, a deadly disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild or severe symptoms, or fatal, depending on many factors such as parasite virulence and host immune status. Malaria can be treated with various drugs, with artemisinin-based combination therapies (ACTs) being the first-line choice. Recent advances in genetics and genomics of malaria parasites have contributed greatly to our understanding of parasite population dynamics, transmission, drug responses, and pathogenesis. However, knowledge gaps in parasite biology and host-parasite interactions still remain. Parasites resistant to multiple antimalarial drugs have emerged, while advanced clinical trials have shown partial efficacy for one available vaccine. Here we discuss genetic and genomic studies of Plasmodium biology, host-parasite interactions, population structures, mosquito infectivity, antigenic variation, and targets for treatment and immunization. Knowledge from these studies will advance our understanding of malaria pathogenesis, epidemiology, and evolution and will support work to discover and develop new medicines and vaccines.


Assuntos
Antimaláricos/farmacologia , Resistência a Medicamentos/genética , Evolução Molecular , Genoma de Protozoário/genética , Malária/epidemiologia , Malária/parasitologia , Plasmodium/efeitos dos fármacos , Plasmodium/genética , Humanos , Plasmodium/classificação , Plasmodium/patogenicidade
8.
Mol Plant Microbe Interact ; 32(10): 1267-1269, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31425006

RESUMO

Phytophthora capsici is an oomycete plant pathogen with a wide host range. Worldwide, P. capsici is known for causing the principal disease of chili pepper crops. Our goal was to expand the available genome resources for this diverse pathogen by generating whole-genome sequences for six isolates of P. capsici from Mexico.


Assuntos
Genoma de Protozoário , Phytophthora , Capsicum/parasitologia , Genoma de Protozoário/genética , México , Phytophthora/genética , Doenças das Plantas/parasitologia
9.
Mol Plant Microbe Interact ; 32(11): 1472-1474, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31306082

RESUMO

The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.


Assuntos
Genoma de Protozoário , Phytophthora , California , Genoma de Protozoário/genética , Phytophthora/genética , Doenças das Plantas/parasitologia , Quercus/parasitologia , Análise de Sequência de DNA
10.
Genome Biol Evol ; 11(7): 1952-1957, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-31218350

RESUMO

Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given that half of its genome is composed of repetitive sequences. Here, we report de novo assemblies, annotation, and comparative analyses of the Berenice strain using a combination of Illumina short reads and MinION long reads. Our work demonstrates that Nanopore sequencing improves T. cruzi assembly contiguity and increases the assembly size in ∼16 Mb. Specifically, we found that assembly improvement also refines the completeness of coding regions for both single-copy genes and repetitive transposable elements. Beyond its historical and epidemiological importance, Berenice constitutes a fundamental resource because it now constitutes a high-quality assembly available for TcII (clade C), a prevalent lineage causing human infections in South America. The availability of Berenice genome expands the known genetic diversity of these parasites and reinforces the idea that T. cruzi is intraspecifically divided in three main clades. Finally, this work represents the introduction of Nanopore technology to resolve complex protozoan genomes, supporting its subsequent application for improving trypanosomatid and other highly repetitive genomes.


Assuntos
Doença de Chagas/parasitologia , Trypanosoma cruzi/genética , Doença de Chagas/genética , Genoma de Protozoário/genética , Sequenciamento de Nucleotídeos em Larga Escala , Nanoporos , Filogenia , Análise de Sequência de DNA
11.
Nucleic Acids Res ; 47(15): 8036-8049, 2019 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-31251800

RESUMO

Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profiling of endogenous sRNAs in context of different transcriptomic states (serotypes). We developed a pipeline to identify, and characterize 2602 siRNA producing clusters (SRCs). Our data show no evidence that SRCs produce miRNAs, and in contrast to other species, no preference for strand specificity of siRNAs. Interestingly, most SRCs overlap coding genes and a separate group show siRNA phasing along the entire open reading frame, suggesting that the mRNA transcript serves as a source for siRNAs. Integrative analysis of siRNA abundance and gene expression levels revealed surprisingly that mRNA and siRNA show negative as well as positive associations. Two RNA-dependent RNA Polymerase mutants, RDR1 and RDR2, show a drastic loss of siRNAs especially in phased SRCs accompanied with increased mRNA levels. Importantly, most SRCs depend on both RDRs, reminiscent to primary siRNAs in the RNAi against exogenous RNA, indicating mechanistic overlaps between exogenous and endogenous RNAi contributing to flexible transcriptome adaptation.


Assuntos
Adaptação Fisiológica/genética , Paramecium/genética , Interferência de RNA , RNA Interferente Pequeno/genética , Transcriptoma , Perfilação da Expressão Gênica , Ontologia Genética , Genoma de Protozoário/genética , MicroRNAs/genética , RNA Mensageiro/genética
12.
Nat Commun ; 10(1): 2665, 2019 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-31209259

RESUMO

Estimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.


Assuntos
Resistência a Medicamentos/genética , Monitoramento Epidemiológico , Genoma de Protozoário/genética , Malária Falciparum/microbiologia , Plasmodium falciparum/genética , Antimaláricos/farmacologia , Antimaláricos/uso terapêutico , Artemisininas/farmacologia , Artemisininas/uso terapêutico , Ásia Sudeste , Biodiversidade , Genótipo , Geografia Médica , Malária Falciparum/tratamento farmacológico , Malária Falciparum/prevenção & controle , Plasmodium falciparum/efeitos dos fármacos , Plasmodium falciparum/isolamento & purificação , Polimorfismo de Nucleotídeo Único
13.
Nucleic Acids Res ; 47(15): 7973-7988, 2019 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-31147720

RESUMO

DNA damage-induced cell cycle checkpoints serve as surveillance mechanisms to maintain genomic stability, and are regulated by ATM/ATR-mediated signaling pathways that are conserved from yeast to humans. Trypanosoma brucei, an early divergent microbial eukaryote, lacks key components of the conventional DNA damage-induced G2/M cell cycle checkpoint and the spindle assembly checkpoint, and nothing is known about how T. brucei controls its cell cycle checkpoints. Here we discover a kinetochore-based, DNA damage-induced metaphase checkpoint in T. brucei. MMS-induced DNA damage triggers a metaphase arrest by modulating the abundance of the outer kinetochore protein KKIP5 in an Aurora B kinase- and kinetochore-dependent, but ATM/ATR-independent manner. Overexpression of KKIP5 arrests cells at metaphase through stabilizing the mitotic cyclin CYC6 and the cohesin subunit SCC1, mimicking DNA damage-induced metaphase arrest, whereas depletion of KKIP5 alleviates the DNA damage-induced metaphase arrest and causes chromosome mis-segregation and aneuploidy. These findings suggest that trypanosomes employ a novel DNA damage-induced metaphase checkpoint to maintain genomic integrity.


Assuntos
Pontos de Checagem do Ciclo Celular/genética , Dano ao DNA , Genoma de Protozoário/genética , Instabilidade Genômica , Cinetocoros/metabolismo , Trypanosoma/genética , Proteínas Mutadas de Ataxia Telangiectasia/genética , Proteínas Mutadas de Ataxia Telangiectasia/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , Ciclinas/genética , Ciclinas/metabolismo , Humanos , Metáfase , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , Trypanosoma/metabolismo , Trypanosoma brucei brucei/genética , Trypanosoma brucei brucei/metabolismo
14.
Nature ; 568(7750): 103-107, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30944491

RESUMO

Apicomplexa is a group of obligate intracellular parasites that includes the causative agents of human diseases such as malaria and toxoplasmosis. Apicomplexans evolved from free-living phototrophic ancestors, but how this transition to parasitism occurred remains unknown. One potential clue lies in coral reefs, of which environmental DNA surveys have uncovered several lineages of uncharacterized basally branching apicomplexans1,2. Reef-building corals have a well-studied symbiotic relationship with photosynthetic Symbiodiniaceae dinoflagellates (for example, Symbiodinium3), but the identification of other key microbial symbionts of corals has proven to be challenging4,5. Here we use community surveys, genomics and microscopy analyses to identify an apicomplexan lineage-which we informally name 'corallicolids'-that was found at a high prevalence (over 80% of samples, 70% of genera) across all major groups of corals. Corallicolids were the second most abundant coral-associated microeukaryotes after the Symbiodiniaceae, and are therefore core members of the coral microbiome. In situ fluorescence and electron microscopy confirmed that corallicolids live intracellularly within the tissues of the coral gastric cavity, and that they possess apicomplexan ultrastructural features. We sequenced the genome of the corallicolid plastid, which lacked all genes for photosystem proteins; this indicates that corallicolids probably contain a non-photosynthetic plastid (an apicoplast6). However, the corallicolid plastid differs from all other known apicoplasts because it retains the four ancestral genes that are involved in chlorophyll biosynthesis. Corallicolids thus share characteristics with both their parasitic and their free-living relatives, which suggests that they are evolutionary intermediates and implies the existence of a unique biochemistry during the transition from phototrophy to parasitism.


Assuntos
Antozoários/parasitologia , Apicomplexa/genética , Apicomplexa/metabolismo , Clorofila/biossíntese , Genes de Protozoários/genética , Filogenia , Animais , Apicomplexa/citologia , Recifes de Corais , Dinoflagelados/citologia , Dinoflagelados/genética , Dinoflagelados/metabolismo , Genoma de Protozoário/genética , Fotossíntese , Plastídeos/genética , Simbiose
15.
Mol Plant Microbe Interact ; 32(9): 1067-1076, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-30951442

RESUMO

Effectors are small, secreted proteins that facilitate infection of host plants by all major groups of plant pathogens. Effector protein identification in oomycetes relies on identification of open reading frames with certain amino acid motifs among additional minor criteria. To date, identification of effectors relies on custom scripts to identify motifs in candidate open reading frames. Here, we developed the R package effectR, which provides a convenient tool for rapid prediction of effectors in oomycete genomes, or with custom scripts for any genome, in a reproducible way. The effectR package relies on a combination of regular expressions statements and hidden Markov model approaches to predict candidate RxLR and crinkler effectors. Other custom motifs for novel effectors can easily be implemented and added to package updates. The effectR package has been validated with published oomycete genomes. This package provides a convenient tool for wet lab researchers interested in reproducible identification of candidate effectors in oomycete genomes.


Assuntos
Motivos de Aminoácidos , Oomicetos , Software , Motivos de Aminoácidos/genética , Genoma de Protozoário/genética , Interações Hospedeiro-Parasita , Oomicetos/genética , Doenças das Plantas/parasitologia , Plantas/parasitologia , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , Software/normas
16.
Proc Natl Acad Sci U S A ; 116(8): 3183-3192, 2019 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-30723152

RESUMO

The positioning of chromosomes in the nucleus of a eukaryotic cell is highly organized and has a complex and dynamic relationship with gene expression. In the human malaria parasite Plasmodium falciparum, the clustering of a family of virulence genes correlates with their coordinated silencing and has a strong influence on the overall organization of the genome. To identify conserved and species-specific principles of genome organization, we performed Hi-C experiments and generated 3D genome models for five Plasmodium species and two related apicomplexan parasites. Plasmodium species mainly showed clustering of centromeres, telomeres, and virulence genes. In P. falciparum, the heterochromatic virulence gene cluster had a strong repressive effect on the surrounding nuclear space, while this was less pronounced in Plasmodium vivax and Plasmodium berghei, and absent in Plasmodium yoelii In Plasmodium knowlesi, telomeres and virulence genes were more dispersed throughout the nucleus, but its 3D genome showed a strong correlation with gene expression. The Babesia microti genome showed a classical Rabl organization with colocalization of subtelomeric virulence genes, while the Toxoplasma gondii genome was dominated by clustering of the centromeres and lacked virulence gene clustering. Collectively, our results demonstrate that spatial genome organization in most Plasmodium species is constrained by the colocalization of virulence genes. P. falciparum and P. knowlesi, the only two Plasmodium species with gene families involved in antigenic variation, are unique in the effect of these genes on chromosome folding, indicating a potential link between genome organization and gene expression in more virulent pathogens.


Assuntos
Genoma de Protozoário/genética , Heterocromatina/genética , Malária Falciparum/genética , Plasmodium falciparum/genética , Animais , Centrômero/genética , Regulação da Expressão Gênica/genética , Genômica , Humanos , Malária Falciparum/parasitologia , Plasmodium berghei/genética , Plasmodium berghei/patogenicidade , Plasmodium falciparum/patogenicidade , Plasmodium knowlesi/genética , Plasmodium knowlesi/patogenicidade , Plasmodium vivax/genética , Plasmodium vivax/patogenicidade , Telômero/genética , Toxoplasma/genética , Toxoplasma/patogenicidade
17.
Parasitol Res ; 118(4): 1299-1306, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30778751

RESUMO

Coccidiosis is recognized as one of the most widespread and pathogenic parasitic infections in migratory waterfowl throughout the world. It can be caused by several species of Eimeria. We sequenced the complete mitochondrial genome (mtDNA) of Eimeria anseris from wintering greater white-fronted geese (Anser albifrons) in China. The complete E. anseris mtDNA is 6179 bp in size and contains three protein-coding genes (CYT B, COI, and COIII), 12 gene fragments for large subunit ribosomal RNA (rRNA), and seven gene fragments for small subunit rRNA, but no transfer RNA genes. Available complete Eimeria mtDNA sequences are highly conserved in sequence: the sequences are all similar in length; with the same three protein-coding genes and fragmented rRNA genes; ATG is generally the start codon, and TAA and TAG are the most frequently used stop codons. Our molecular phylogenetic analyses show some species clustering into host-specific clades, but many species do not follow clear coevolutionary host segregating patterns. The results suggest that Eimeria spp. from turkeys and chickens are paraphyletic groups, while Eimeria species isolated from rabbits are a monophyletic group. E. anseris, which infects A. albifrons, and another group of Eimeria isolated from chickens form a closely related monophyletic clade.


Assuntos
Coccidiose/veterinária , DNA Mitocondrial/genética , Eimeria/genética , Genoma Mitocondrial/genética , Genoma de Protozoário/genética , Animais , Galinhas/parasitologia , China , Coccidiose/parasitologia , Eimeria/isolamento & purificação , Gansos/parasitologia , Lagos/parasitologia , Filogenia , Coelhos , Perus/parasitologia
18.
Mol Plant Microbe Interact ; 32(8): 1047-1060, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30794480

RESUMO

Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.


Assuntos
Variações do Número de Cópias de DNA , Genoma de Protozoário , Phytophthora , Polimorfismo Genético , Genoma de Protozoário/genética , Haplótipos , Phytophthora/genética
19.
Nat Commun ; 10(1): 371, 2019 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-30670687

RESUMO

Studies of Plasmodium vivax gene expression are complicated by the lack of in vitro culture system and the difficulties associated with studying clinical infections that often contain multiple clones and a mixture of parasite stages. Here, we characterize the transcriptomes of P. vivax parasites from 26 malaria patients. We show that most parasite mRNAs derive from trophozoites and that the asynchronicity of P. vivax infections is therefore unlikely to confound gene expression studies. Analyses of gametocyte genes reveal two distinct clusters of co-regulated genes, suggesting that male and female gametocytes are independently regulated. Finally, we analyze gene expression changes induced by chloroquine and show that this antimalarial drug efficiently eliminates most P. vivax parasite stages but, in contrast to P. falciparum, does not affect trophozoites.


Assuntos
Cloroquina/farmacologia , Regulação da Expressão Gênica/efeitos dos fármacos , Plasmodium vivax/efeitos dos fármacos , Plasmodium vivax/genética , Transcriptoma/efeitos dos fármacos , Antimaláricos/farmacologia , Ciclo Celular/efeitos dos fármacos , Ciclo Celular/genética , Feminino , Genes de Protozoários/efeitos dos fármacos , Genes de Protozoários/genética , Genoma de Protozoário/efeitos dos fármacos , Genoma de Protozoário/genética , Humanos , Malária/tratamento farmacológico , Malária Falciparum/tratamento farmacológico , Malária Vivax/tratamento farmacológico , Masculino , Família Multigênica , Plasmodium falciparum/efeitos dos fármacos , Plasmodium falciparum/genética , Plasmodium vivax/patogenicidade , RNA Mensageiro/metabolismo , Trofozoítos/efeitos dos fármacos , Trofozoítos/genética
20.
Parasitol Res ; 118(2): 715-721, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30607610

RESUMO

Parasites of managed bees can disrupt the colony success of the host, but also influence local bee-parasite dynamics, which is regarded as a threat for wild bees. Therapeutic measures have been suggested to improve the health of managed bees, for instance, exploiting the bees' RNA interference (RNAi) pathway to treat against viral pathogens. Gut trypanosomes are an important group of bee parasites in at least two common managed bee species, i.e., managed Apis mellifera and reared Bombus terrestris. In several trypanosomes, RNAi activity is present, while in other associated genes of RNAi, such as Dicer-like (DCL) and Argonaute (AGO), it is lost. Up to date, the ability to exploit the RNAi of gut trypanosomes of bees has remained unexplored. Here, we screened parasite genomes of two honey bee protozoa (Crithidia mellificae and Lotmaria passim) and two bumble bee protozoa (Crithidia bombi and Crithidia expoeki) for the presence of DCL and AGO proteins. For C. mellificae, we constructed a double-stranded RNA (dsRNA) targeting kinetoplastid membrane protein-11 (KMP-11) to test the RNAi potential to kill this parasite. Transfection with KMP-11 dsRNA, but also adding it to the growth medium resulted in small growth reduction of the trypanosome C. mellificae, thereby showing the limited potential to apply dsRNA therapeutics to control trypanosome infection in managed honey bee species. Within bumble bees, there seems to be no application potentials against C. bombi, as we could only retrieve non-functional DCL- and AGO-related genes within the genome of this bumble bee parasite.


Assuntos
Proteínas Argonauta/genética , Abelhas/parasitologia , Crithidia/crescimento & desenvolvimento , Infecções por Euglenozoa/terapia , RNA Interferente Pequeno/uso terapêutico , Ribonuclease III/genética , Trypanosomatina/crescimento & desenvolvimento , Animais , Crithidia/genética , Infecções por Euglenozoa/parasitologia , Genoma de Protozoário/genética , Interferência de RNA , RNA de Cadeia Dupla/genética , RNA Interferente Pequeno/genética , Trypanosomatina/genética
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