Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 12.879
Filtrar
1.
Mol Genet Genomics ; 295(1): 221-231, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31641857

RESUMO

The Xinjiang Uyghur Autonomous Region of China (XUARC) with 47 ethnic groups is a very colorful ethnic region of China, harboring abundant genetic and cultural diversity. The Kazakhs are the third largest ethnic group (7.02%) after Uyghur (46.42%) and Han (38.99%) in Xinjiang, but their genetic diversity and forensic characterization are poorly understood. In the current study, we genotyped 15 autosomal short tandem repeat (STR) loci and ten Y-STRs in 889 individuals (659 male and 230 female) collected from Kazak population of the Ili Kazak Autonomous Prefecture using AGCU Expressmarker 16 and 10Y-STR Kit (EX16 + 10Y). For autosomal STRs, we observed a total of 174 different alleles ranging from 6 to 34.2 repeat units and FGA showed the greatest power of discrimination (20 alleles) in Ili Kazakh population. We have not observed departures from Hardy-Weinberg equilibrium (HWE) after sequential Bonferroni correction and only found a minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The combined power of exclusion (CPE) was 0.99999998395 and combined power of discrimination (CPD) was 99.999999999999999798%. For Y-STRs, we observed a total of 496 different haplotypes in these ten Y-STR loci. The gene diversities ranged from 0.5023 (DYS391) to 0.8357 (DYS385a/b). The overall haplotype diversity (GD) was 0.9985 with random matching probability (RMP) of 0.0015. The results of population genetic analysis based on both autosomal and Y-chromosome STRs demonstrated that the genetic affinity among populations is generally consistent with ethnic, linguistic, and continental geographical classifications.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Cromossomos/genética , Polimorfismo Genético/genética , Alelos , Feminino , Frequência do Gene/genética , Testes Genéticos/métodos , Genética Populacional/métodos , Haplótipos/genética , Humanos , Masculino , Repetições de Microssatélites/genética , Filogenia
2.
Mol Genet Genomics ; 295(1): 107-120, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31506717

RESUMO

The oriental gall wasp Dryocosmus kuriphilus represents a limiting pest for the European Chestnut (Castanea sativa, Fagaceae) as it creates severe yield losses. The European Chestnut is a deciduous tree, having major social, economic and environmental importance in Southern Europe, covering an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Cultivars show different susceptibility and very few are resistant to gall wasp. To deeply investigate the plant response and understand which factors can lead the plant to develop or not the gall, the study of transcriptome is basic (fundamental). To date, little transcriptomic information are available for C. sativa species. Hence, we present a de novo assembly of the chestnut transcriptome of the resistant Euro-Japanese hybrid 'Bouche de Bétizac' (BB) and the susceptible cultivar 'Madonna' (M), collecting RNA from buds at different stages of budburst. The two transcriptomes were assembled into 34,081 (BB) and 30,605 (M) unigenes, respectively. The former was used as a reference sequence for further characterization analyses, highlighting the presence of 1444 putative resistance gene analogs (RGAs) and about 1135 unigenes, as putative MiRNA targets. A global quantitative transcriptome profiling comparing the resistant and the susceptible cultivars, in the presence or not of the gall wasp, revealed some GO enrichments as "response to stimulus" (GO:0050896), and "developmental processes" (e.g., post-embryonic development, GO:0009791). Many up-regulated genes appeared to be transcription factors (e.g., RAV1, AP2/ERF, WRKY33) or protein regulators (e.g., RAPTOR1B) and storage proteins (e.g., LEA D29) involved in "post-embryonic development". Our analysis was able to provide a large amount of information, including 7k simple sequence repeat (SSR) and 335k single-nucleotide polymorphism (SNP)/INDEL markers, and generated the first reference unigene catalog for the European Chestnut. The transcriptome data for C. sativa will contribute to understand the genetic basis of the resistance to gall wasp and will provide useful information for next molecular genetic studies of this species and its relatives.


Assuntos
Fagaceae/genética , Transcriptoma/genética , Vespas/patogenicidade , Animais , Europa (Continente) , Fagaceae/parasitologia , Perfilação da Expressão Gênica/métodos , Repetições de Microssatélites/genética , Anotação de Sequência Molecular/métodos , Doenças das Plantas/parasitologia , Polimorfismo de Nucleotídeo Único/genética , Fatores de Transcrição/genética , Árvores/genética , Árvores/parasitologia , Regulação para Cima/genética
3.
Nat Genet ; 51(11): 1652-1659, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31676866

RESUMO

Short tandem repeats (STRs) have been implicated in a variety of complex traits in humans. However, genome-wide studies of the effects of STRs on gene expression thus far have had limited power to detect associations and provide insights into putative mechanisms. Here, we leverage whole-genome sequencing and expression data for 17 tissues from the Genotype-Tissue Expression Project to identify more than 28,000 STRs for which repeat number is associated with expression of nearby genes (eSTRs). We use fine-mapping to quantify the probability that each eSTR is causal and characterize the top 1,400 fine-mapped eSTRs. We identify hundreds of eSTRs linked with published genome-wide association study signals and implicate specific eSTRs in complex traits, including height, schizophrenia, inflammatory bowel disease and intelligence. Overall, our results support the hypothesis that eSTRs contribute to a range of human phenotypes, and our data should serve as a valuable resource for future studies of complex traits.


Assuntos
Regulação da Expressão Gênica , Genoma Humano , Estudo de Associação Genômica Ampla , Repetições de Microssatélites/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Estatura/genética , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Doenças Inflamatórias Intestinais/genética , Inteligência/genética , Esquizofrenia/genética
4.
Parasitol Res ; 118(12): 3371-3375, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31705288

RESUMO

Enterocytozoon bieneusi is a single-celled obligate pathogen that seriously threatens animal and public health. However, information on the prevalence and genotypes of E. bieneusi in alpacas in China is limited. In the present study, 366 fresh fecal samples from alpacas in Shanxi Province, northern China, were collected to detect E. bieneusi by nested PCR amplification of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA). The overall prevalence of E. bieneusi in alpacas was 4.4% (16/366), including 3.9% (12/305) in Yangqu County and 6.6% (4/61) in Dai county, respectively. Four known genotypes were identified, namely ALP1, ALP3, P, and SH11, all of which belong to the zoonotic group 1 by phylogenetic analysis. Moreover, ITS-positive samples were further characterized by PCR amplification of other four targets, including three microsatellites (MS1, MS3, and MS7) and one minisatellite (MS4). Multilocus sequence typing (MLST) showed that 5, 2, 3, and 3 types were identified at MS1, MS3, MS7, and MS4 loci, respectively, representing eight multilocus genotypes (MLGs). These findings contribute to the improved understanding of the prevalence and genotypes of E. bieneusi in alpacas in China and have important implications for controlling E. bieneusi infections in animals and humans.


Assuntos
Camelídeos Americanos/parasitologia , DNA Intergênico/genética , Enterocytozoon/genética , Repetições de Microssatélites/genética , Microsporidiose/veterinária , Doenças Parasitárias em Animais/parasitologia , Animais , China/epidemiologia , Enterocytozoon/classificação , Enterocytozoon/isolamento & purificação , Fezes/parasitologia , Genótipo , Humanos , Microsporidiose/epidemiologia , Tipagem de Sequências Multilocus , Filogenia , Reação em Cadeia da Polimerase , Prevalência
5.
Vet Parasitol ; 276: 108965, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31726324

RESUMO

Tritrichomonas foetus isolates from feline and bovine origin has been previously shown to carry a certain degree of genetic heterogeneity. Here, novel candidate molecular markers were developed by means of multilocus sequence typing of the gap2 gene (encoding for T. foetus glyceraldehyde-3-phosphate dehydrogenase), ITS region, the TR7/TR8 variable-length repeat and microsatellite genotyping. These markers were used to characterize T. foetus field isolates from bulls and domestic cats and to compare phylogenetically with the following ATCC isolates: T. foetus isolated from cattle and pig (syn. Tritrichomonas suis), Tritrichomonas mobilensis, Tetratrichomonas gallinarum and Pentatrichomonas hominis. Among them, TFMS10 and TFMS7 were found to be the most polymorphic markers. Moreover, an 809 bp fragment of the gap2 gene was successfully amplified from all the trichomonads included in this study and the sequence analysis revealed differences between T. foetus porcine and feline genotypes and T. mobilensis in comparison to the bovine T. foetus ATCC isolate. The TR7/TR8 repeat pattern was not reproducible, being only consistent the fragments of approximately 110 and 217 bp. Sequence analysis of the latter revealed the existence of 3 SNPs resulting in 98.6 % homology between bovine and feline isolates. A search for similar sequences was carried out to develop a Restriction Length Fragment Polymorphism analysis. A 503 bp region, named TF1, revealed the existence of two BbvI restriction enzyme sites that were able to generate different length fragments for T. foetus feline and bovine isolates. Finally, the neighbour-joining analyses showed that T. foetus porcine genotype clusters together with bovine genotype, whereas T. mobilensis and the feline genotype form a separate cluster.


Assuntos
Doenças do Gato/parasitologia , Doenças dos Bovinos/parasitologia , Marcadores Genéticos , Infecções Protozoárias em Animais/parasitologia , Tritrichomonas foetus/genética , Animais , Sequência de Bases , Gatos , Bovinos , Sequência Consenso , DNA Ribossômico/química , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/genética , Masculino , Repetições de Microssatélites/genética , Repetições Minissatélites , Dados de Sequência Molecular , Tipagem de Sequências Multilocus/veterinária , Filogenia , Polimorfismo de Fragmento de Restrição , Polimorfismo de Nucleotídeo Único , Sequências Repetitivas de Ácido Nucleico/genética , Alinhamento de Sequência/veterinária , Tritrichomonas foetus/classificação
6.
Nat Biotechnol ; 37(12): 1478-1481, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31740840

RESUMO

Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods1-4. Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorithm for raw signal analysis. Our method, termed STRique for short tandem repeat identification, quantification and evaluation, integrates conventional sequence mapping of nanopore reads with raw signal alignment for the localization of repeat boundaries and a hidden Markov model-based repeat counting mechanism. We demonstrate the precise quantification of repeat numbers in conjunction with the determination of CpG methylation states in the repeat expansion and in adjacent regions at the single-molecule level without amplification. Our method enables the study of previously inaccessible genomic regions and their epigenetic marks.


Assuntos
Metilação de DNA/genética , Genômica/métodos , Repetições de Microssatélites/genética , /métodos , Algoritmos , Esclerose Amiotrófica Lateral/genética , Proteína C9orf72/genética , Sistemas CRISPR-Cas/genética , Células Cultivadas , Humanos , Nanoporos
7.
BMC Plant Biol ; 19(1): 504, 2019 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-31744457

RESUMO

BACKGROUND: The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect. Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood. RESULTS: Here, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect. Arachis species into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts and A. monticola that are the only tetraploid (AABB) species within Arachis are nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species. CONCLUSION: In summary, we have acquired sequences of twelve complete Arachis cp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.


Assuntos
Arachis/genética , Variação Genética , Genoma de Cloroplastos/genética , Alelos , Mutação INDEL , Repetições de Microssatélites/genética , Filogenia , Melhoramento Vegetal
8.
J Cancer Res Clin Oncol ; 145(12): 2891-2899, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31617076

RESUMO

PURPOSE: Microsatellites are widely distributed repetitive DNA motifs, accounting for approximately 3% of the genome. Due to mismatch repair system deficiency, insertion or deletion of repetitive units often occurs, leading to microsatellite instability. In this review, we aimed to explore the relationship between MSI and biological behaviour of colorectal carcinoma, gastric carcinoma, lymphoma/leukaemia and endometrial carcinoma, as well as the application of frameshift peptide vaccines in cancer therapy. METHODS: The relevant literature from PubMed and Baidu Xueshu were reviewed in this article. The ClinicalTrials.gov database was searched for clinical trials related to the specific topic. RESULTS: Microsatellite instability is divided into three subtypes: high-level, low-level microsatellite instability, and stable microsatellites. The majority of tumour patients with high-level microsatellite instability often show a better efficacy and prognosis than those with low-level microsatellite instability or stable microsatellites. In coding regions, especially for genes involved in tumourigenesis, microsatellite instability often results in inactivation of proteins and contributes to tumourigenesis. Moreover, the occurrence of microsatellite instability in coding regions can also cause the generation of frameshift peptides that are thought to be unknown and novel to the individual immune system. Thus, these frameshift peptides have the potential to be biomarkers to raise tumour-specific immune responses. CONCLUSION: MSI has the potential to become a key predictor for evaluating the degree of malignancy, efficacy and prognosis of tumours. Clinically, MSI patterns will provide more valuable information for clinicians to create optimal individualized treatment strategies based on frameshift peptides vaccines.


Assuntos
Mutação da Fase de Leitura/genética , Repetições de Microssatélites/genética , Neoplasias/genética , Animais , Carcinogênese/genética , Ensaios Clínicos como Assunto , Reparo de Erro de Pareamento de DNA/genética , Humanos , Instabilidade de Microssatélites , Prognóstico
9.
Genes Dev ; 33(23-24): 1635-1640, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31624084

RESUMO

Short tandem repeats (STRs) are prone to expansion mutations that cause multiple hereditary neurological and neuromuscular diseases. To study pathomechanisms using mouse models that recapitulate the tissue specificity and developmental timing of an STR expansion gene, we used rolling circle amplification and CRISPR/Cas9-mediated genome editing to generate Dmpk CTG expansion (CTGexp) knockin models of myotonic dystrophy type 1 (DM1). We demonstrate that skeletal muscle myoblasts and brain choroid plexus epithelial cells are particularly susceptible to Dmpk CTGexp mutations and RNA missplicing. Our results implicate dysregulation of muscle regeneration and cerebrospinal fluid homeostasis as early pathogenic events in DM1.


Assuntos
Processamento Alternativo/genética , Repetições de Microssatélites/genética , Músculo Esquelético/fisiopatologia , Distrofia Miotônica/genética , Distrofia Miotônica/fisiopatologia , Processamento de RNA/genética , Regiões 3' não Traduzidas/genética , Animais , Plexo Corióideo/fisiopatologia , Proteínas de Ligação a DNA/genética , Modelos Animais de Doenças , Regulação da Expressão Gênica no Desenvolvimento , Técnicas de Introdução de Genes , Camundongos , Fibras Musculares Esqueléticas/citologia , Fibras Musculares Esqueléticas/patologia , Músculo Esquelético/citologia , Mutação , Miotonina Proteína Quinase/genética , Miotonina Proteína Quinase/metabolismo , Proteínas de Ligação a RNA/genética
10.
Plant Dis ; 103(11): 2751-2758, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31509494

RESUMO

Didymella pisi is the primary causal pathogen of Ascochyta blight (AB) of dry pea in Montana. Diagnosis of AB is challenging because there are six different species that cause AB worldwide and that can co-occur. Additionally, agar plate identification of D. pisi is challenging due to its slow growth rate. Currently, there are no PCR-based assays developed for specific detection of D. pisi or any fungal pathogen in the AB complex of dry pea. In this study, we evaluated simple sequence repeat (SSR) primer pairs for their specificity and sensitivity in real-time and conventional SSR-PCR both in vitro and in planta. The specificity of the assay was determined by testing DNA of 10 dry pea varieties, fungal species in the AB complex, and fungal species associated with dry pea. To avoid false-negative results, plant and fungal DNA markers were included as controls in a conventional multiplex SSR-PCR, to amplify any plant or fungal DNA in the absence of the D. pisi SSR target. SYBR Green SSR-quantitative PCR (qPCR) detection was conducted using the same primer pairs but in a uniplex format. D. pisi was specifically amplified, whereas other fungi and host DNA were not. Also, sensitivity experiments showed that the detection limit was 0.01 ng of DNA of D. pisi for both assays and 100 conidia in SSR-qPCR. These assays are valuable diagnostic tools for the detection of D. pisi.


Assuntos
Ascomicetos , Técnicas Microbiológicas , Ervilhas , Reação em Cadeia da Polimerase , Ascomicetos/genética , Limite de Detecção , Técnicas Microbiológicas/métodos , Repetições de Microssatélites/genética , Montana , Ervilhas/microbiologia
11.
J Appl Microbiol ; 127(6): 1814-1823, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31517423

RESUMO

AIM: The aims of this study were to identify races and mating types of Setosphaeria turcica causing northern corn leaf blight in Heilongjiang province of China and analyse the genetic diversity of S. turcica isolates using SSR markers. METHODS AND RESULTS: Based on gene-for-gene interactions, 13 races of S. turcica (races 0, 1, 2, 3, 12, 13, 23, 123, N, 1N, 12N, 3N and 23N) were isolated from infected corn plants in Heilongjiang province. Races 0 and 1 were the predominant races, and race 23N was identified for the first time in the region. Using two pairs of specific primers, three mating types, 'a', 'Aa' and 'A', were identified, with 'a' being the predominant mating type. SSR markers were used to analyse genetic diversity of 60 S. turcica isolates. Five SSR primers were polymorphic, which resulted in 45 reproducible bands with 2-15 bands for each primer. Cluster analysis separated the isolates into five groups at a similarity coefficient of 0·84. Analysis of molecular variance showed that there was significant correlation between SSR groups and mating type of the isolates. No significant correlation was found between SSR groups and physiological races or geographical location of the isolates. CONCLUSIONS: The work reported that races 0 and 1 were the predominant races, and race 23N was identified for the first time in Heilongjiang province with 'a' being the predominant mating type. There was significant correlation between SSR groups and mating type of S. turcica isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results provide information on population structure and genetic diversity of S. turcica causing Northern corn leaf blight, which will facilitate the development of effective disease management programs.


Assuntos
Ascomicetos/genética , Variação Genética , Doenças das Plantas/microbiologia , Zea mays/microbiologia , Ascomicetos/classificação , China , Análise por Conglomerados , Genes Fúngicos/genética , Genes Fúngicos Tipo Acasalamento/genética , Repetições de Microssatélites/genética
12.
Nat Commun ; 10(1): 4128, 2019 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-31511524

RESUMO

Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.


Assuntos
Mutação em Linhagem Germinativa/genética , Neoplasias/genética , Neoplasias/terapia , Animais , Proteínas de Ciclo Celular , Linhagem Celular Tumoral , Proliferação de Células , Sobrevivência Celular , Quinase 2 Dependente de Ciclina/antagonistas & inibidores , Quinase 2 Dependente de Ciclina/metabolismo , Regulação Neoplásica da Expressão Gênica , Células HEK293 , Humanos , Camundongos , Repetições de Microssatélites/genética , Proteínas de Neoplasias/metabolismo , Proteínas de Fusão Oncogênica/metabolismo , Fenótipo , Polimorfismo Genético , Transativadores , Resultado do Tratamento , Regulação para Cima/genética
13.
An Acad Bras Cienc ; 91(3): e20180749, 2019 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-31531533

RESUMO

Due to the increasing search for renewable resources, plant fibers have become an alternative when creating new products. Studies demonstrate the potential use of pineapple fibers in composites. The objective of this work was to evaluate the genetic diversity and verify any association between ISSR (Inter Simple Sequence Repeats) bands and quality of pineapple fibers for use in cements in the civil construction. The study analyzed the genetic variability of 11 pineapple genotypes, as well as the possible association of 131 bands from 16 ISSR markers with fiber quality characteristics. Eleven bands were selected based on their high correlations (0.64578* to 0.72457*) with three fiber quality variables. Of these, two bands were purified, sequenced, and blasted against sequences in GenBank at NCBI. These markers can be used in marker assisted selection to genetically improve the quality of pineapple fiber. Bands that returned no hits in the NCBI BLAST search can be deposited as new sequences in the GenBank. Therefore, the SCAR markers, once validated, can be useful in pineapple genetic breeding programs worldwide by using molecular marker assisted selection for fiber resistance, which could subsidize the development of more promising genotypes for industrial use and contribute to the sustainability of this new production sector.


Assuntos
Ananas/genética , Marcadores Genéticos , Repetições de Microssatélites/genética , Cruzamento , Variação Genética , Genótipo , Filogenia , Polimorfismo Genético , Estatísticas não Paramétricas
14.
BMC Evol Biol ; 19(1): 181, 2019 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-31533616

RESUMO

BACKGROUND: Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on their occurrence. For this reason we present here an overview of the distribution and properties of satellites in a set of representative species. Our results provide novel insights into the evolutionary relationship between eukaryotes, Archaea and Bacteria. RESULTS: We have searched all possible satellites present in the NCBI reference group of genomes in Archaea (142 species) and in Bacteria (119 species), detecting 2735 satellites in Archaea and 1067 in Bacteria. We have found that the distribution of satellites is very variable in different organisms. The archaeal Methanosarcina class stands out for the large amount of satellites in their genomes. Satellites from a few species have similar characteristics to those in eukaryotes, but most species have very few satellites: only 21 species in Archaea and 18 in Bacteria have more than 4 satellites/Mb. The distribution of satellites in these species is reminiscent of what is found in eukaryotes, but we find two significant differences: most satellites have a short length and many of them correspond to segments of genes coding for amino acid repeats. Transposition of non-coding satellites throughout the genome occurs rarely: only in the bacteria Leptospira interrogans and the archaea Methanocella conradii we have detected satellite families of transposed satellites with long repeats. CONCLUSIONS: Our results demonstrate that the presence of satellites in the genome is not an exclusive feature of eukaryotes. We have described a few prokaryotes which do contain satellites. We present a discussion on their eventual evolutionary significance.


Assuntos
DNA Satélite/genética , Células Procarióticas/metabolismo , Archaea/genética , Bactérias/genética , Repetições de Microssatélites/genética , Filogenia
15.
BMC Evol Biol ; 19(1): 183, 2019 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-31533625

RESUMO

BACKGROUND: Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew severely affects yield security wheat production in China. Understanding the virulence structure and genetic variations of this pathogen is important for breeding wheat lines resistant to wheat powdery mildew. However, information related to genes controlling resistance remains elusive. This study analyzes the virulence structure and the genetic diversity of pathogenic Bgt populations isolated from northeastern (Liaoning, Heilongjiang) and northwestern (Gansu) China, two representative wheat producing areas, on 37 wheat cultivars each carrying a known powdery mildew resistance (Pm) gene. RESULTS: Bgt isolates from northeastern China show higher frequencies of virulence genes than populations from Gansu Province. Many of the known Pm genes failed to provide resistance in this study. However, Pm21 provided 100% resistance to all isolates from all three provinces, obtained during two consecutive years, while Pm13 provided 100% resistance in Gansu. Pm13, Pm16, Pm18, and Pm22 also showed partial resistance in northeastern China, while Pm16, Pm18, Pm22, Pm5 + 6 and Pm2 + 6 +? maintained some resistance in Gansu. Genetic diversity among populations in different regions was detected by cluster analyses using expressed sequence tag-simple sequence repeat (EST-SSR). When the genetic similarity coefficient is relatively high, populations from the same regional origin are mostly clustered into one group while populations from different regions exhibit large genetic differences. CONCLUSION: Pm21 remains the best choice for breeding programs to maintain resistance to Bgt. Only 58% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and frequency of virulence gene data.


Assuntos
Ascomicetos/genética , Ascomicetos/patogenicidade , Variação Genética , Ascomicetos/isolamento & purificação , China , Análise por Conglomerados , Etiquetas de Sequências Expressas , Frequência do Gene , Genes Fúngicos , Repetições de Microssatélites/genética , Filogenia , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Triticum/genética , Triticum/microbiologia , Virulência/genética
16.
Nat Commun ; 10(1): 4240, 2019 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-31534121

RESUMO

Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation.


Assuntos
Especiação Genética , Smegmamorpha/classificação , Smegmamorpha/genética , Simpatria/genética , Animais , DNA Mitocondrial/genética , Fluxo Gênico , Genética Populacional , Genoma/genética , Lagos , Repetições de Microssatélites/genética , Mitocôndrias/genética , Polimorfismo de Nucleotídeo Único/genética , Rios
17.
Int J Mol Sci ; 20(17)2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31480228

RESUMO

Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational and commercial value. The arid landscape over much of these fishes' range, coupled with the boom and bust hydrology of their habitat, means that these species have potential to provide useful evolutionary insights, such as karyotypes and sex chromosome evolution in vertebrates. Here we applied standard and molecular cytogenetic techniques to characterise karyotypes for golden perch and Murray cod. Both species have a diploid chromosome number 2n = 48 and a male heterogametic sex chromosome system (XX/XY). While the karyotype of golden perch is composed exclusively of acrocentric chromosomes, the karyotype of Murray cod consists of two submetacentric and 46 subtelocentric/acrocentric chromosomes. We have identified variable accumulation of repetitive sequences (AAT)10 and (CGG)10 along with diverse methylation patterns, especially on the sex chromosomes in both species. Our study provides a baseline for future cytogenetic analyses of other Australian freshwater fishes, especially species from the family Percichthyidae, to better understand their genome and sex chromosome evolution.


Assuntos
Água Doce , Cariótipo , Percas/genética , Perciformes/genética , Cromossomos Sexuais/genética , Animais , Bandeamento Cromossômico , Metilação de DNA/genética , Feminino , Geografia , Masculino , Metáfase , Repetições de Microssatélites/genética , Filogenia , Especificidade da Espécie , Telômero/genética
18.
Plant Sci ; 287: 110204, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31481207

RESUMO

Stripe rust (Yr), caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a devastating foliar disease of wheat in China. Chinese wheat landraces originating from the middle and lower reaches of the Yangtze River are potential stripe-rust resistance resources. To identify APR genes for stripe-rust resistance, a panel of 188 accessions derived from the middle and lower reaches of the Yangtze River were inoculated with a mixture of Chinese P. striiformis f. sp. tritici races and resistance evaluated under field conditions in five environments at adult-plant stages. Seventy-three accessions showed degrees of stable resistance. Combining phenotypic datasets from multiple field experiments with high-quality Diversity Arrays Technology and simple sequence repeat markers, we detected 21 marker-trait associations spanning 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6B, and 6D, respectively. Single QTLs explained 9.67% to 16.14% of the observed phenotypic variation. Nine QTLs co-localized with previously reported Yr genes or genomic regions. The remaining QTLs were potential novel loci associated with adult-stage stripe-rust resistance. Two novel QTLs, QYr.sicau-3B.2 and QYr.sicau-5B.3, located on chromosomes 3B and 5B significantly explained 16.14% and 11.16% of the phenotypic variation, respectively. Haplotype analysis revealed that accessions carrying APR variants or their combinations showed enhanced degrees of resistance. The potentially novel loci or genomic regions associated with adult-stage resistance may be useful to improve stripe-rust resistance in current wheat cultivars and for future isolation of stripe-rust resistance genes.


Assuntos
Basidiomycota/fisiologia , Resistência à Doença/genética , Estudo de Associação Genômica Ampla , Doenças das Plantas/imunologia , Locos de Características Quantitativas/genética , Triticum/genética , China , Loci Gênicos/genética , Marcadores Genéticos/genética , Haplótipos , Repetições de Microssatélites/genética , Fenótipo , Doenças das Plantas/microbiologia , Triticum/imunologia , Triticum/microbiologia
19.
Zhonghua Liu Xing Bing Xue Za Zhi ; 40(8): 992-996, 2019 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-31484267

RESUMO

Objective: To analyze the genetic diversity of Aedes albopictus populations in the coastal areas of southern China by using the microsatellite markers to provide a basis for the control of vectors. Methods: Genetic diversity and clustering analysis of Aedes albopictus populations were studied in the 7 microsatellite loci, in Hangzhou, Ningbo and Yiwu of Zhejiang province, Longyan of Fujian province, Guangzhou of Guangdong province, Nanning of Guangxi Zhuang Autonomous Region and Haikou of Hainan province. Results: Numbers of different alleles (5.429-7.571), effective alleles (2.897-3.632), allele richness (5.236-7.170) and expected heterozygosity (0.538- 0.637) were detected from each of the Aedes albopictus population by using 7 microsatellite markers. The inbreeding coefficients appeared as 0.008-0.332, with heterozygote deficiency, in these populations. Fixation index of the whole populations was 0.058, suggesting that the genetic variation among the 7 populations was 5.8%. Data from the Neighbor-Joining clustering analysis showed that populations from Hangzhou and Yiwu belonged to one branch while Longyan and Guangzhou populations constituted another branch. Aedes albopictus populations of Nanning and Haikou showed great genetic variation but formed a single branch. Bayesian analysis on Aedes albopictus populations showed that the possible number of clusters was 3. Conclusions: Based on 7 microsatellite loci, relatively high genetic diversity and medium level of genetic differentiation that increasing with the geographical distances, were found in these Aedes albopictus populations, from the coastal areas in southern China.


Assuntos
Aedes/genética , Variação Genética , Repetições de Microssatélites , Aedes/classificação , Animais , Teorema de Bayes , China , Repetições de Microssatélites/genética , Mosquitos Vetores , Filogenia
20.
Cytogenet Genome Res ; 158(3): 160-169, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31394537

RESUMO

The discovery of sex chromosome systems in non-model organisms has elicited growing recognition that sex chromosomes evolved via diverse paths that are not fully elucidated. Lineages with labile sex determination, such as turtles, hold critical cues, yet data are skewed toward hide-neck turtles (suborder Cryptodira) and scant for side-neck turtles (suborder Pleurodira). Here, we used classic and molecular cytogenetics to investigate Emydura subglobosa (ESU), an unstudied side-neck turtle with genotypic sex determination from the family Chelidae, where extensive morphological divergence exists among XX/XY systems. Our data represent the first cytogenetic description for ESU. Similarities were found between ESU and E. macquarii (EMA), such as identical chromosome number (2n = 50), a single and dimorphic nucleolus organizer region (NOR) localized in a microchromosome pair (ESU14) of both sexes (detected via FISH of 18S rDNA). Only the larger NOR is active (detected by silver staining). As in EMA, comparative genome hybridization revealed putative macro XX/XY chromosomes in ESU (the 4th largest pair). Our comparative analyses and revaluation of previous data strongly support the hypothesis that Emydura's XX/XY system evolved via fusion of an ancestral micro-Y (retained by Chelodina longicollis) onto a macro-autosome. This evolutionary trajectory differs from the purported independent evolution of XX/XY from separate ancestral autosomes in Chelodina and Emydura that was previously reported. Our data permit dating this Y-autosome fusion to at least the split of Emydura around 45 Mya and add critical information about the evolution of the remarkable diversity of sex-determining mechanisms in turtles, reptiles, and vertebrates.


Assuntos
Evolução Molecular , Cromossomos Sexuais/genética , Tartarugas/genética , Animais , Hibridização Genômica Comparativa , Hibridização in Situ Fluorescente , Cariótipo , Masculino , Repetições de Microssatélites/genética , RNA Ribossômico 18S/genética , Coloração pela Prata , Tartarugas/classificação
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA