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1.
Appl Microbiol Biotechnol ; 103(17): 7111-7128, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31273397

RESUMO

The fungus Isaria javanica is an important entomopathogen that parasitizes various insects and is effective for pest control. In this study, we sequenced and assembled the genomes (IJ1G and IJ2G) of two I. javanica strains isolated from different insects. The genomes were approximately 35 Mb in size with 11,441 and 11,143 protein-coding genes, respectively. Using a phylogenomic approach, we evaluated genome evolution across five entomopathogenic fungi in Cordycipitaceae. By comparative genome analysis, it was found that family S53 serine peptidases were expanded in Cordycipitaceae entomopathogens, particularly in I. javanica. Gene duplication events were identified based on phylogenetic relationships inferred from 82 S53 peptidases within six entomopathogenic fungal genomes. Moreover, we found that carbohydrate-active enzymes and proteinases were the largest secretory protein groups encoded in the I. javanica genome, especially chitinases (GH18), serine and aspartic peptidases (S53, S08, S10, A01). Pathogenesis-related genes and genes for bacterial-like toxins and secondary metabolites were also identified. By comparative transcriptome analysis, differentially expressed genes in response to insect nutrients (in vitro) were identified. Moreover, most S53 peptidases were detected to be significantly upregulated during the initial fungal infection process in insects (in vivo) by RT-qPCR. Our results provide new clues about understanding evolution of pathogenic proteases and may suggest that abundant S53 peptidases in the I. javanica genome may contribute to its effective parasitism on various insects.

2.
J Agric Food Chem ; 67(26): 7266-7273, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31244199

RESUMO

Chemical investigation of fungus Pochonia chlamydosporia strain 170, derived from rice fermentation sediment samples, afforded seven radicicol analogues, including two new compounds, monocillin VI (1) and monocillin VII (2), and five known compounds, monocillin II (3), monorden D (4), monocillin IV (5), monocillin V (6), and pochonin M (7). The structures of compounds 1-7 were established primarily by analysis of nuclear magnetic resonance data, and the absolute configurations of the secondary alcohol in compounds 1 and 2 were assigned by the modified Mosher method. All seven compounds have modest antibacterial activities, with a minimal inhibitory concentration (MIC) of 25.6 µg/mL for compounds 1 and 3-7 and 51.2 µg/mL for compound 2, on inhibition of the growth of the plant pathogen Xanthomonas campestris (the positive control ampicillin showed a MIC value of 12.8 µg/mL), indicating that the fungus has the potential to control bacterial disease. The biosynthetic gene cluster and putative biosynthetic pathways of these radicicol analogues in the P. chlamydosporia genome were proposed. These findings increase our knowledge of the chemical potential of P. chlamydosporia and may allow us to better utilize the fungus as a biological control agent.


Assuntos
Antibacterianos/química , Hypocreales/metabolismo , Macrolídeos/química , Antibacterianos/biossíntese , Antibacterianos/farmacologia , Vias Biossintéticas , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Hypocreales/química , Hypocreales/genética , Macrolídeos/metabolismo , Macrolídeos/farmacologia , Testes de Sensibilidade Microbiana , Família Multigênica , Xanthomonas campestris/efeitos dos fármacos , Xanthomonas campestris/crescimento & desenvolvimento
3.
Sci Rep ; 8(1): 7256, 2018 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-29740007

RESUMO

Root-knot nematodes (RKNs) are highly specialized parasites that interact with their host plants using a range of strategies. The esophageal glands are the main places where nematodes synthesize effector proteins, which play central roles in successful invasion. The Meloidogyne incognita effector MiISE5 is exclusively expressed within the subventral esophageal cells and is upregulated during early parasitic stages. In this study, we show that MiISE5 can be secreted to barley cells through infectious hyphae of Magnaporthe oryzae. Transgenic Arabidopsis plants expressing MiISE5 became significantly more susceptible to M. incognita. Inversely, the tobacco rattle virus (TRV)-mediated silence of MiISE5 decreased nematode parasitism. Moreover, transient expression of MiISE5 suppressed cell death caused by Burkholderia glumae in Nicotiana benthamiana. Based on transcriptome analysis of MiISE5 transgenic sample and the wild-type (WT) sample, we obtained 261 DEGs, and the results of GO and KEGG enrichment analysis indicate that MiISE5 can interfere with various metabolic and signaling pathways, especially the JA signaling pathway, to facilitate nematode parasitism. Results from the present study suggest that MiISE5 plays an important role during the early stages of parasitism and provides evidence to decipher the molecular mechanisms underlying the manipulation of host immune defense responses by M. incognita.

4.
Front Plant Sci ; 9: 252, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29628931

RESUMO

Meloidogyne incognita is highly specialized parasite that interacts with host plants using a range of strategies. The effectors are synthesized in the esophageal glands and secreted into plant cells through a needle-like stylet during parasitism. In this study, based on RNA-seq and bioinformatics analysis, we predicted 110 putative Meloidogyne incognita effectors that contain nuclear localization signals (NLSs). Combining the Burkholderia glumae-pEDV based screening system with subcellular localization, from 20 randomly selected NLS effector candidates, we identified an effector MiISE6 that can effectively suppress B. glumae-induced cell death in Nicotiana benthamiana, targets to the nuclei of plant cells, and is highly expressed in early parasitic J2 stage. Sequence analysis showed that MiISE6 is a 157-amino acid peptide, with an OGFr_N domain and two NLS motifs. Hybridization in situ verified that MiISE6 is expressed in the subventral esophageal glands. Yeast invertase secretion assay validated the function of the signal peptide harbored in MiISE6. Transgenic Arabidopsis thaliana plants expressing MiISE6 become more susceptible to M. incognita. Inversely, the host-derived RNAi of MiISE6 of the nematode can decrease its parasitism on host. Based on transcriptome analysis of the MiISE6 transgenic Arabidopsis samples and the wild-type samples, we obtained 852 differentially expressed genes (DEGs). Integrating Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, we found that expression of MiISE6 in Arabidopsis can suppress jasmonate signaling pathway. In addition, the expression of genes related to cell wall modification and the ubiquitination proteasome pathway also have detectable changes in the transgenic plants. Results from the present study suggest that MiISE6 is involved in interaction between nematode-plant, and plays an important role during the early stages of parasitism by interfering multiple signaling pathways of plant. Moreover, we found homologs of MiISE6 in other sedentary nematodes, Meloidogyne hapla and Globodera pallida. Our experimental results provide evidence to decipher the molecular mechanisms underlying the manipulation of host immune defense responses by plant parasitic nematodes, and transcriptome data also provide useful information for further study nematode-plant interactions.

5.
Sci Rep ; 8(1): 1123, 2018 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-29348510

RESUMO

Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode. We focus on secretomes of the fungus, which play important roles in pathogenicity and fungus-host/environment interactions, and identified 1,750 secreted proteins, with a high proportion of carboxypeptidases, subtilisins, and chitinases. We analyzed the phylogenies of these genes and predicted new pathogenic molecules. By comparative transcriptome analysis, we found that secreted proteins involved in responses to nutrient stress are mainly comprised of proteases and glycoside hydrolases. Moreover, 32 secreted proteins undergoing positive selection and 71 duplicated gene pairs encoding secreted proteins are identified. Two duplicated pairs encoding secreted glycosyl hydrolases (GH30), which may be related to fungal endophytic process and lost in many insect-pathogenic fungi but exist in nematophagous fungi, are putatively acquired from bacteria by horizontal gene transfer. The results help understanding genetic origins and evolution of parasitism-related genes.


Assuntos
Hypocreales/genética , Hypocreales/metabolismo , Metaboloma , Proteoma , Transcriptoma , Cromossomos Fúngicos , Biologia Computacional/métodos , Duplicação Gênica , Transferência Genética Horizontal , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Interações Hospedeiro-Parasita , Interações Hospedeiro-Patógeno , Filogenia , Plantas/microbiologia , Plantas/parasitologia , Seleção Genética
6.
Artigo em Inglês | MEDLINE | ID: mdl-26709967

RESUMO

Lecanicillium saksenae CGMCC5329 is a useful biological control agent against plant-parasitic nematodes. The complete mitogenome sequence of L. saksenae is reported for the first time. The mitochondrial genome is 25 919 bp long with 14 typical protein-coding genes, an intronic ORF coding for a putative ribosomal protein (rps3), 2 ribosomal RNA genes and a set of 26 transfer RNA genes. The phylogeny based on 12 protein-coding genes (except the loss of other two genes in Acremonium implicatum) suggests the close phylogenetic relationship between L. saksenae and L. muscarium. Comparative analysis reveals that mitogenome of L. saksenae is 1420 bp larger than L. muscarium, mainly due to the intergenic region between cox2 and trnR. The trnC between cob and cox1 is conserved in the mitogenomes of three nematophagous fungus of Pochonia chlamydosporia, A. implicatum and L. saksenae, but absent in L. muscarium. This study may provide valuable information for further research on mitochondrial evolution of nematophagous fungus and Lecanicillium species.


Assuntos
Genoma Mitocondrial , Hypocreales/genética , DNA Intergênico/química , DNA Intergênico/genética , DNA Mitocondrial/química , DNA Mitocondrial/isolamento & purificação , DNA Mitocondrial/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Hypocreales/classificação , Fases de Leitura Aberta/genética , Filogenia , RNA Ribossômico/química , RNA Ribossômico/genética , RNA de Transferência/química , RNA de Transferência/genética , Análise de Sequência de DNA
7.
PLoS Pathog ; 12(7): e1005685, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-27416025

RESUMO

Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. However, how the fungus functions at the molecular level remains unknown. Here, we sequenced two isolates (PLBJ-1 and PLFJ-1) of P. lilacinum from different places Beijing and Fujian. Genomic analysis showed high synteny of the two isolates, and the phylogenetic analysis indicated they were most related to the insect pathogen Tolypocladium inflatum. A comparison with other species revealed that this fungus was enriched in carbohydrate-active enzymes (CAZymes), proteases and pathogenesis related genes. Whole genome search revealed a rich repertoire of secondary metabolites (SMs) encoding genes. The non-ribosomal peptide synthetase LcsA, which is comprised of ten C-A-PCP modules, was identified as the core biosynthetic gene of lipopeptide leucinostatins, which was specific to P. lilacinum and T. ophioglossoides, as confirmed by phylogenetic analysis. Furthermore, gene expression level was analyzed when PLBJ-1 was grown in leucinostatin-inducing and non-inducing medium, and 20 genes involved in the biosynthesis of leucionostatins were identified. Disruption mutants allowed us to propose a putative biosynthetic pathway of leucinostatin A. Moreover, overexpression of the transcription factor lcsF increased the production (1.5-fold) of leucinostatins A and B compared to wild type. Bioassays explored a new bioactivity of leucinostatins and P. lilacinum: inhibiting the growth of Phytophthora infestans and P. capsici. These results contribute to our understanding of the biosynthetic mechanism of leucinostatins and may allow us to utilize P. lilacinum better as bio-control agent.


Assuntos
Paecilomyces/genética , Paecilomyces/metabolismo , Peptídeos/metabolismo , Phytophthora/microbiologia , Cromatografia Líquida de Alta Pressão , Perfilação da Expressão Gênica , Genes Fúngicos , Genômica , Análise de Sequência com Séries de Oligonucleotídeos , Controle Biológico de Vetores/métodos , Filogenia , Reação em Cadeia da Polimerase , Transcriptoma
8.
DNA Res ; 2016 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-27374612

RESUMO

MicroRNAs (miRNAs) are ∼22 nucleotide non-coding RNAs that regulate gene expression by targeting mRNAs for degradation or inhibiting protein translation. To investigate whether miRNAs regulate the pathogenesis in necrotrophic fungus Rhizoctonia solani AG1 IA, which causes significant yield loss in main economically important crops, and to determine the regulatory mechanism occurring during pathogenesis, we constructed hyphal small RNA libraries from six different infection periods of the rice leaf. Through sequencing and analysis, 177 miRNA-like small RNAs (milRNAs) were identified, including 15 candidate pathogenic novel milRNAs predicted by functional annotations of their target mRNAs and expression patterns of milRNAs and mRNAs during infection. Reverse transcription-quantitative polymerase chain reaction results for randomly selected milRNAs demonstrated that our novel comprehensive predictions had a high level of accuracy. In our predicted pathogenic protein-protein interaction network of R. solani, we added the related regulatory milRNAs of these core coding genes into the network, and could understand the relationships among these regulatory factors more clearly at the systems level. Furthermore, the putative pathogenic Rhi-milR-16, which negatively regulates target gene expression, was experimentally validated to have regulatory functions by a dual-luciferase reporter assay. Additionally, 23 candidate rice miRNAs that may involve in plant immunity against R. solani were discovered. This first study on novel pathogenic milRNAs of R. solani AG1 IA and the recognition of target genes involved in pathogenicity, as well as rice miRNAs, participated in defence against R. solani could provide new insights into revealing the pathogenic mechanisms of the severe rice sheath blight disease.

9.
DNA Res ; 23(3): 241-51, 2016 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-27098848

RESUMO

Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm.


Assuntos
Algoritmos , Elementos de DNA Transponíveis , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Magnaporthe/genética , Polimorfismo Genético , Análise de Sequência de DNA/métodos , DNA Fúngico/química , DNA Fúngico/genética , Genoma Fúngico
10.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(5): 3246-7, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-25630733

RESUMO

The complete mitochondrial genome of the nematophagous fungus Acremonium implicatum is reported for the first time. The genome is concatenated with 22,367 bp in length, encoding 13 protein-coding genes, 2 ribosomal RNA genes and a set of 17 transfer RNA genes. The synteny analysis reveals that 50.35% of A. implicatum mitochondrial sequences matched to 48.21% of Acremonium chrysogenum mitochondrial sequences with 85.68% identity. Two proteins of cox3 and nad6, as well as seven tRNAs are lost in A. implicatum mitogenome compared to A. chrysogenum mitogenome. The gene orders in A. implicatum and A. chrysogenum mitogenome is different, which is mainly due to the location of nad4 and cox2. In addition, one transposition event related to tRNAs is identified in these two mitogenomes. This study may provide valuable mitochondrial information for research on A. implicatum and facilitate the study of mitochondrial evolution.


Assuntos
Acremonium/genética , Genoma Mitocondrial , Acremonium/classificação , Composição de Bases , Códon , Genes Mitocondriais , Tamanho do Genoma , Fases de Leitura Aberta , Sequências Reguladoras de Ácido Nucleico , Análise de Sequência de DNA , Sintenia , Sequenciamento Completo do Genoma
11.
BMC Microbiol ; 15: 5, 2015 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-25636983

RESUMO

BACKGROUND: The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales. RESULTS: The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae. CONCLUSIONS: We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales.


Assuntos
DNA Fúngico/genética , DNA Mitocondrial/genética , Genoma Mitocondrial , Hypocreales/classificação , Hypocreales/genética , Análise por Conglomerados , DNA Fúngico/química , DNA Mitocondrial/química , Ordem dos Genes , Genes Fúngicos , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Homologia de Sequência , Sintenia
12.
Microbiol Res ; 170: 18-26, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25458554

RESUMO

The nematophagous fungus Pochonia chlamydosporia, which belongs to the family Clavicipitaceae (Ascomycota: Pezizomycotina: Sordariomycetes: Hypocreales), is a promising biological control agent for root-knot and cyst nematodes. Its biocontrol effect has been confirmed by pot and field trials. The genome sequence of the fungus was completed recently; therefore, genome-wide functional analyses will identify its infection-associated genes. Gene knockout techniques are useful molecular tools to study gene functions. However, cultures of P. chlamydosporia are resistant to high levels of a range of fungal inhibitors, which makes the gene knockout technique difficult in this fungus. Fortunately, we found that the wild P. chlamydosporia strain PC-170 could not grow on medium containing 150µgml(-1) G418 sulfate, representing a new selectable marker for P. chlamydosporia. The neomycin-resistance gene (neo), which was amplified from the plasmid pKOV21, conferred G418-resistance on the fungus; therefore, it was chosen as the marker gene. We subsequently developed a gene knockout system for P. chlamydosporia using split-marker homologous recombination cassettes with resistance selection and protoplast transformation. The split-marker cassettes were developed using fusion PCR, and involved only two rounds of PCR. The final products comprised two linear constructs. Each construct contained a flanking region of the target gene and two thirds of the neo gene. Alkaline serine protease and chitinase were confirmed to be produced by P. chlamydosporia during infection of nematode eggs and could participate in lysis of the eggshell of nematode eggs. Here, we knocked out one chitinase gene, VFPPC_01099, and two protease genes (VFPPC_10088, VFPPC_06535). We obtained approximately 100 suspected mutants after each transformation. After screening by PCR, the average rate of gene knockout was 13%: 11% (VFPPC_01099), 13% (VFPPC_10088) and 15% (VFPPC_06535). This efficient and convenient technique will accelerate functional genomic studies in P. chlamydosporia.


Assuntos
Técnicas de Inativação de Genes , Hypocreales/genética , Fungicidas Industriais/farmacologia , Hypocreales/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Mutação , Protoplastos , Transfecção/métodos , Transformação Genética
13.
J Proteome Res ; 13(7): 3277-93, 2014 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-24894516

RESUMO

Rhizoctonia solani is the major pathogenic fungi of rice sheath blight. It is responsible for the most serious disease of rice (Oryza sativa L.) and causes significant yield losses in rice-growing countries. Identifying the protein-protein interaction (PPI) maps of R. solani can provide insights into the potential pathogenic mechanisms and assign putative functions to unknown genes. Here, we exploited a PPI map of R. solani anastomosis group 1 IA (AG-1 IA) based on the interolog and domain-domain interaction methods. We constructed a core subset of high-confidence protein networks consisting of 6705 interactions among 1773 proteins. The high quality of the network was revealed by comprehensive methods, including yeast two-hybrid experiments. Pathogenic interaction subnetwork, secreted proteins subnetwork, and mitogen-activated protein kinase (MAPK) cascade subnetwork and their interacting partners were constructed and analyzed. Moreover, to exactly predict the pathogenic factors, the expression levels of the interaction proteins were investigated by analyzing RNA sequences that consisted of samples from the entire infection progress. The PPIs offer an exceptionally rich source of data that can be used to understand the gene functions and biological processes of this serious disease at the system level.


Assuntos
Proteínas Fúngicas/fisiologia , Oryza/microbiologia , Doenças das Plantas/microbiologia , Rhizoctonia/metabolismo , Proteínas Fúngicas/química , Sistema de Sinalização das MAP Quinases , Anotação de Sequência Molecular , Domínios e Motivos de Interação entre Proteínas , Mapeamento de Interação de Proteínas , Mapas de Interação de Proteínas , Transcriptoma
14.
Nat Commun ; 4: 1424, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23361014

RESUMO

Rhizoctonia solani is a major fungal pathogen of rice (Oryza sativa L.) that causes great yield losses in all rice-growing regions of the world. Here we report the draft genome sequence of the rice sheath blight disease pathogen, R. solani AG1 IA, assembled using next-generation Illumina Genome Analyser sequencing technologies. The genome encodes a large and diverse set of secreted proteins, enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, which probably reflect an exclusive necrotrophic lifestyle. We find few repetitive elements, a closer relationship to Agaricomycotina among Basidiomycetes, and expand protein domains and families. Among the 25 candidate pathogen effectors identified according to their functionality and evolution, we validate 3 that trigger crop defence responses; hence we reveal the exclusive expression patterns of the pathogenic determinants during host infection.


Assuntos
Evolução Biológica , Oryza/microbiologia , Doenças das Plantas/microbiologia , Rhizoctonia/genética , Rhizoctonia/patogenicidade , Evolução Molecular , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Regulação Fúngica da Expressão Gênica , Genes Fúngicos/genética , Dados de Sequência Molecular , Fenótipo , Filogenia , Folhas de Planta/microbiologia , Sequências Repetitivas de Ácido Nucleico/genética , Reprodutibilidade dos Testes , Análise de Sequência de DNA , Transdução de Sinais/genética , Soja/microbiologia , Transcriptoma/genética , Fatores de Virulência/metabolismo , Zea mays/microbiologia
15.
Sci China Life Sci ; 53(1): 107-111, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-20596962

RESUMO

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.


Assuntos
Cromossomos Artificiais Bacterianos/genética , Biblioteca Genômica , Análise de Sequência de DNA/métodos , Ursidae/genética , Animais , Gatos , Clonagem Molecular , Cães , Evolução Molecular , Humanos , Camundongos , Dados de Sequência Molecular , Filogenia , RNA não Traduzido/classificação , RNA não Traduzido/genética , Sequências Repetitivas de Ácido Nucleico/genética
16.
Nature ; 463(7279): 311-7, 2010 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-20010809

RESUMO

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.


Assuntos
Genoma/genética , Genômica , Ursidae/genética , Algoritmos , Animais , China , Sequência Conservada/genética , Mapeamento de Sequências Contíguas , Dieta/veterinária , Cães , Evolução Molecular , Feminino , Fertilidade/genética , Fertilidade/fisiologia , Heterozigoto , Humanos , Família Multigênica/genética , Polimorfismo de Nucleotídeo Único/genética , Receptores Acoplados a Proteínas-G/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Sintenia/genética , Ursidae/classificação , Ursidae/fisiologia
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