Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 31.092
Filtrar
1.
Am J Hum Genet ; 106(4): 525-534, 2020 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-32220293

RESUMO

Despite next-generation sequencing, which now allows for the accurate detection of segmental aneuploidies from in vitro fertilization embryo biopsies, the origin and characteristics of these aneuploidies are still relatively unknown. Using a multifocal biopsy approach (four trophectoderms [TEs] and one inner cell mass [ICM] analyzed per blastocyst; n = 390), we determine the origin of the aneuploidy and the diagnostic predictive value of segmental aneuploidy detection in TE biopsies toward the ICM's chromosomal constitution. Contrary to the prevalent meiotic origin of whole-chromosome aneuploidies, we show that sub-chromosomal abnormalities in human blastocysts arise from mitotic errors in around 70% of cases. As a consequence, the positive-predictive value toward ICM configuration was significantly lower for segmental as compared to whole-chromosome aneuploidies (70.8% versus 97.18%, respectively). In order to enhance the clinical utility of reporting segmental findings in clinical TE biopsies, we have developed and clinically verified a risk stratification model based on a second TE biopsy confirmation and segmental length; this model can significantly improve the prediction of aneuploidy risk in the ICM in over 86% of clinical cases enrolled. In conclusion, we provide evidence of the predominant mitotic origin of segmental aneuploidies in preimplantation embryos and develop a risk stratification model that can help post-test genetic counseling and that facilitates the decision-making process on clinical utilization of these embryos.


Assuntos
Blastocisto/fisiologia , Embrião de Mamíferos/fisiologia , Desenvolvimento Embrionário/genética , Aneuploidia , Aberrações Cromossômicas , Cromossomos/genética , Hibridização Genômica Comparativa/métodos , Feminino , Fertilização In Vitro/métodos , Humanos , Incidência , Gravidez , Diagnóstico Pré-Implantação/métodos
2.
Am J Hum Genet ; 106(4): 426-437, 2020 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-32169169

RESUMO

Segments of identity by descent (IBD) are used in many genetic analyses. We present a method for detecting identical-by-descent haplotype segments in phased genotype data. Our method, called hap-IBD, combines a compressed representation of haplotype data, the positional Burrows-Wheeler transform, and multi-threaded execution to produce very fast analysis times. An attractive feature of hap-IBD is its simplicity: the input parameters clearly and precisely define the IBD segments that are reported, so that program correctness can be confirmed by users. We evaluate hap-IBD and four state-of-the-art IBD segment detection methods (GERMLINE, iLASH, RaPID, and TRUFFLE) using UK Biobank chromosome 20 data and simulated sequence data. We show that hap-IBD detects IBD segments faster and more accurately than competing methods, and that hap-IBD is the only method that can rapidly and accurately detect short 2-4 centiMorgan (cM) IBD segments in the full UK Biobank data. Analysis of 485,346 UK Biobank samples through the use of hap-IBD with 12 computational threads detects 231.5 billion autosomal IBD segments with length ≥2 cM in 24.4 h.


Assuntos
Genoma Humano/genética , Análise de Sequência de DNA/métodos , Alelos , Cromossomos/genética , Simulação por Computador , Análise de Dados , Marcadores Genéticos/genética , Genética Populacional/métodos , Genótipo , Haplótipos/genética , Humanos , Polimorfismo de Nucleotídeo Único/genética , Software
3.
Cytogenet Genome Res ; 160(2): 94-99, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32062647

RESUMO

In this study, we analyzed the karyotype of Salvator merianae (Teiidae) from the Brazilian semiarid region using different cytogenetic markers. Chromosomes were examined by classical (Giemsa and AgNOR staining) and molecular (FISH with ribosomal, telomeric, and microsatellite probes) cytogenetic approaches. S. merianae showed a diploid chromosome number of 2n = 38 (10 biarmed macrochromosomes + 28 microchromosomes). No sex-linked chromosome heteromorphisms were observed. Clusters of 18S/28S rDNA were localized in the terminal region of the long arm of pair 2. In addition to the typical telomeric signals, (TTAGGG)n repeats were detected in the pericentromeric region of some macrochromosome pairs, which might indicate the occurrence of chromosomal rearrangements via chromosome fusions. Hybridization signals of the microsatellite probes (GA)n, (GAA)n, and (GAG)n were uniformly distributed across all chromosomes, while (CA)n, (CAA)n, and (CAC)n produced brighter signals in the telomeric and pericentromeric regions of specific chromosome pairs. The comparison with previous studies demonstrates that, despite the wide distribution of S. merianae, the macrostructure organization of the karyotype remained unchanged, showing stability in diploid number and chromosome morphology.


Assuntos
Análise Citogenética/veterinária , Cariotipagem/veterinária , Lagartos/genética , Animais , Cromossomos/genética , Diploide , Evolução Molecular , Feminino , Cariótipo , Masculino
4.
BMC Bioinformatics ; 21(1): 73, 2020 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-32093610

RESUMO

BACKGROUND: The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dynamics and scale. However, a variety of recent assays, in particular Hi-C, have generated new details of chromatin structure, spawning a number of novel biological findings. Many findings have resulted from analyses on the level of native contact data as generated by the assays. Alternatively, reconstruction based approaches often proceed by first converting contact frequencies into distances, then generating a three dimensional (3D) chromatin configuration that best recapitulates these distances. Subsequent analyses can enrich contact level analyses via superposition of genomic attributes on the reconstruction. But, such advantages depend on the accuracy of the reconstruction which, absent gold standards, is inherently difficult to assess. Attempts at accuracy evaluation have relied on simulation and/or FISH imaging that typically features a handful of low resolution probes. While newly advanced multiplexed FISH imaging offers possibilities for refined 3D reconstruction accuracy evaluation, availability of such data is limited due to assay complexity and the resolution thereof is appreciably lower than the reconstructions being assessed. Accordingly, there is demand for new methods of reconstruction accuracy appraisal. RESULTS: Here we explore the potential of recently proposed stationary distributions, hereafter StatDns, derived from Hi-C contact matrices, to serve as a basis for reconstruction accuracy assessment. Current usage of such StatDns has focussed on the identification of highly interactive regions (HIRs): computationally defined regions of the genome purportedly involved in numerous long-range intra-chromosomal contacts. Consistent identification of HIRs would be informative with respect to inferred 3D architecture since the corresponding regions of the reconstruction would have an elevated number of k nearest neighbors (kNNs). More generally, we anticipate a monotone decreasing relationship between StatDn values and kNN distances. After initially evaluating the reproducibility of StatDns across replicate Hi-C data sets, we use this implied StatDn - kNN relationship to gauge the utility of StatDns for reconstruction validation, making recourse to both real and simulated examples. CONCLUSIONS: Our analyses demonstrate that, as constructed, StatDns do not provide a suitable measure for assessing the accuracy of 3D genome reconstructions. Whether this is attributable to specific choices surrounding normalization in defining StatDns or to the logic underlying their very formulation remains to be determined.


Assuntos
Cromatina/química , Cromossomos , Genoma , Genômica/métodos , Conformação Molecular , Reprodutibilidade dos Testes
6.
Chemosphere ; 249: 126182, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32078850

RESUMO

An adverse tendency induced by the environmental estrogens in female reproductive health is one serious problem worldwide. Diethylstilbestrol (DES), as a synthetic estrogen, is still used as an animal growth stimulant in terrestrial livestock and aquaculture illegally. It has been reported to negatively affect ovarian function and oogenesis. Nevertheless, the mechanism and toxicity of DES on oocyte meiotic maturation are largely unknown. Herein, we found that DES (40 µM) intervened in mouse oocyte maturation and first polar body extrusion (PBE) was decreased in vitro. Cell cycle analysis showed meiotic process was disturbed with oocytes arrested at metaphase I (MI) stage after DES exposure. Further study showed that DES exposure disrupted the spindle assembly and chromosome alignment, which then continuously provoke the spindle assemble checkpoint (SAC). We also observed that the acetylation levels of α-tubulin were dramatically increased in DES-treated oocytes. In addition, the dynamics of actin were also affected. Moreover, the distribution patterns of estrogen receptor α (ERα) were altered in DES-treated oocyte, as indicated by the significant signals accumulation in the spindle area. However, ERα inhibitor failed to rescue the defects of oocyte maturation caused by DES. Of note, the same phenomenon was observed in estrogen-treated oocytes. Collectively, we showed that DES exposure lead to the oocyte meiotic failure via impairing the spindle assembly and chromosome alignment. Our research is helpful to understand how environmental estrogen affects female germ cells and contribute to design the potential therapies to preserve fertility especially for occupational exposure.


Assuntos
Dietilestilbestrol/toxicidade , Estrogênios não Esteroides/toxicidade , Animais , Processos de Crescimento Celular , Cromossomos , Feminino , Pontos de Checagem da Fase M do Ciclo Celular , Meiose/efeitos dos fármacos , Metáfase , Camundongos , Oócitos/metabolismo , Oogênese/efeitos dos fármacos , Fuso Acromático , Testes de Toxicidade , Tubulina (Proteína)/metabolismo
7.
Nat Rev Genet ; 21(5): 311-331, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32051563

RESUMO

RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.


Assuntos
Cromossomos , Interferência de RNA , Animais , Proteínas Argonauta/genética , Centrômero , RNA Helicases DEAD-box/genética , Evolução Molecular , Humanos , Ribonuclease III/genética
8.
Nat Protoc ; 15(3): 840-876, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31969721

RESUMO

Simultaneous observation of 3D chromatin organization and transcription at the single-cell level and with high spatial resolution may hold the key to unveiling the mechanisms regulating embryonic development, cell differentiation and even disease. We recently developed Hi-M, a technology that enables the sequential labeling, 3D imaging and localization of multiple genomic DNA loci, together with RNA expression, in single cells within whole, intact Drosophila embryos. Importantly, Hi-M enables simultaneous detection of RNA expression and chromosome organization without requiring sample unmounting and primary probe rehybridization. Here, we provide a step-by-step protocol describing the design of probes, the preparation of samples, the stable immobilization of embryos in microfluidic chambers, and the complete procedure for image acquisition. The combined RNA/DNA fluorescence in situ hybridization procedure takes 4-5 d, including embryo collection. In addition, we describe image analysis software to segment nuclei, detect genomic spots, correct for drift and produce Hi-M matrices. A typical Hi-M experiment takes 1-2 d to complete all rounds of labeling and imaging and 4 additional days for image analysis. This technology can be easily expanded to investigate cell differentiation in cultured cells or organization of chromatin within complex tissues.


Assuntos
Cromossomos , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Processamento de Imagem Assistida por Computador , Transcrição Genética/fisiologia , Animais , Cromatina , DNA/química , DNA/genética , DNA/metabolismo , Drosophila/embriologia , Corantes Fluorescentes , Hibridização in Situ Fluorescente/métodos , RNA/química , RNA/genética , RNA/metabolismo
9.
Nat Protoc ; 15(3): 991-1012, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31980751

RESUMO

Fit-Hi-C is a programming application to compute statistical confidence estimates for Hi-C contact maps to identify significant chromatin contacts. By fitting a monotonically non-increasing spline, Fit-Hi-C captures the relationship between genomic distance and contact probability without any parametric assumption. The spline fit together with the correction of contact probabilities with respect to bin- or locus-specific biases accounts for previously characterized covariates impacting Hi-C contact counts. Fit-Hi-C is best applied for the study of mid-range (e.g., 20 kb-2 Mb for human genome) intra-chromosomal contacts; however, with the latest reimplementation, named FitHiC2, it is possible to perform genome-wide analysis for high-resolution Hi-C data, including all intra-chromosomal distances and inter-chromosomal contacts. FitHiC2 also offers a merging filter module, which eliminates indirect/bystander interactions, leading to significant reduction in the number of reported contacts without sacrificing recovery of key loops such as those between convergent CTCF binding sites. Here, we describe how to apply the FitHiC2 protocol to three use cases: (i) 5-kb resolution Hi-C data of chromosome 5 from GM12878 (a human lymphoblastoid cell line), (ii) 40-kb resolution whole-genome Hi-C data from IMR90 (human lung fibroblast), and (iii) budding yeast whole-genome Hi-C data at a single restriction cut site (EcoRI) resolution. The procedure takes ~12 h with preprocessing when all use cases are run sequentially (~4 h when run parallel). With the recent improvements in its implementation, FitHiC2 (8 processors and 16 GB memory) is also scalable to genome-wide analysis of the highest resolution (1 kb) Hi-C data available to date (~48 h with 32 GB peak memory). FitHiC2 is available through Bioconda, GitHub and the Python Package Index.


Assuntos
Cromossomos/química , Animais , Sítios de Ligação , Cromatina , Análise por Conglomerados , Bases de Dados Genéticas , Genoma , Genômica , Humanos , Camundongos , Software
10.
Nat Commun ; 11(1): 301, 2020 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-31949148

RESUMO

Speciation is associated with substantial rewiring of the regulatory circuitry underlying the expression of genes. Determining which changes are relevant and underlie the emergence of the human brain or its unique susceptibility to neural disease has been challenging. Here we annotate changes to gene regulatory elements (GREs) at cell type resolution in the brains of multiple primate species spanning most of primate evolution. We identify a unique set of regulatory elements that emerged in hominins prior to the separation of humans and chimpanzees. We demonstrate that these hominin gains perferentially affect oligodendrocyte function postnatally and are preferentially affected in the brains of autism patients. This preference is also observed for human-specific GREs suggesting this system is under continued selective pressure. Our data provide a roadmap of regulatory rewiring across primate evolution providing insight into the genomic changes that underlie the emergence of the brain and its susceptibility to neural disease.


Assuntos
Transtorno Autístico/metabolismo , Encéfalo/metabolismo , Hominidae/metabolismo , Oligodendroglia/metabolismo , Sequências Reguladoras de Ácido Nucleico/fisiologia , Animais , Transtorno Autístico/genética , Callithrix , Cromatina , Imunoprecipitação da Cromatina , Cromossomos/química , Suscetibilidade a Doenças , Evolução Molecular , Feminino , Regulação da Expressão Gênica , Genômica , Hominidae/genética , Humanos , Macaca mulatta , Pan troglodytes
11.
Yi Chuan ; 42(1): 87-99, 2020 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-31956099

RESUMO

The spatial interaction of chromosomes is regarded as an important issue affecting the regulation of gene expression, and the high-throughput chromosome conformation capture (Hi-C) technology has become the primary tool to explore the temporal and spatial interactions of chromosomes in three-dimensional genomics. With the continuous accumulation of Hi-C samples and the increasing complexity of pipelines, the bioinformatic analysis of Hi-C data has been considered an opportunity and a challenge for understanding the spatial regulation mechanism of gene expression. In this paper, the current status and development outline of bioinformatic methods for Hi-C data are introduced, including data normalization, multi-level structure analysis, data visualization and 3D modeling, especially of multi-level structure at A/B compartments, topological associated domains (TADs) and chromain looping levels. Based on this, we provide the outlook of future hotspots and trends in this area. Hopefully our insight will be beneficial for the exploration of gene expression regulation from the traditional linear model to the 3D mode.


Assuntos
Cromossomos/química , Biologia Computacional , Genômica , Cromatina/química
12.
Genome Biol ; 21(1): 11, 2020 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-31937349

RESUMO

Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C's resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI's superiority to existing approaches. In addition, HIFI's restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.


Assuntos
Algoritmos , Cromossomos , DNA/metabolismo , Genoma , Mapeamento por Restrição , Animais , Humanos , Camundongos
14.
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
15.
Cell Mol Life Sci ; 77(1): 61-79, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31728577

RESUMO

Telomeres are protein-DNA complexes that protect chromosome ends from illicit ligation and resection. Telomerase is a ribonucleoprotein enzyme that synthesizes telomeric DNA to counter telomere shortening. Human telomeres are composed of complexes between telomeric DNA and a six-protein complex known as shelterin. The shelterin proteins TRF1 and TRF2 provide the binding affinity and specificity for double-stranded telomeric DNA, while the POT1-TPP1 shelterin subcomplex coats the single-stranded telomeric G-rich overhang that is characteristic of all our chromosome ends. By capping chromosome ends, shelterin protects telomeric DNA from unwanted degradation and end-to-end fusion events. Structures of the human shelterin proteins reveal a network of constitutive and context-specific interactions. The shelterin protein-DNA structures reveal the basis for both the high affinity and DNA sequence specificity of these interactions, and explain how shelterin efficiently protects chromosome ends from genome instability. Several protein-protein interactions, many provided by the shelterin component TIN2, are critical for upholding the end-protection function of shelterin. A survey of these protein-protein interfaces within shelterin reveals a series of "domain-peptide" interactions that allow for efficient binding and adaptability towards new functions. While the modular nature of shelterin has facilitated its part-by-part structural characterization, the interdependence of subunits within telomerase has made its structural solution more challenging. However, the exploitation of several homologs in combination with recent advancements in cryo-EM capabilities has led to an exponential increase in our knowledge of the structural biology underlying telomerase function. Telomerase homologs from a wide range of eukaryotes show a typical retroviral reverse transcriptase-like protein core reinforced with elements that deliver telomerase-specific functions including recruitment to telomeres and high telomere-repeat addition processivity. In addition to providing the template for reverse transcription, the RNA component of telomerase provides a scaffold for the catalytic and accessory protein subunits, defines the limits of the telomeric repeat sequence, and plays a critical role in RNP assembly, stability, and trafficking. While a high-resolution definition of the human telomerase structure is only beginning to emerge, the quick pace of technical progress forecasts imminent breakthroughs in this area. Here, we review the structural biology surrounding telomeres and telomerase to provide a molecular description of mammalian chromosome end protection and end replication.


Assuntos
Telomerase/metabolismo , Proteínas de Ligação a Telômeros/metabolismo , Telômero/metabolismo , Aminopeptidases/química , Aminopeptidases/metabolismo , Animais , Cromossomos/química , Cromossomos/metabolismo , Dipeptidil Peptidases e Tripeptidil Peptidases/química , Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Humanos , Modelos Moleculares , Conformação Proteica , Serina Proteases/química , Serina Proteases/metabolismo , Telomerase/química , Telômero/química , Proteínas de Ligação a Telômeros/química
16.
Nat Rev Genet ; 21(4): 207-226, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31848476

RESUMO

Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.


Assuntos
Cromossomos/química , Núcleo Celular/genética , Cromatina/química , Imunoprecipitação da Cromatina , Genômica/métodos , Humanos , Hibridização in Situ Fluorescente
17.
Zool Res ; 41(1): 94-96, 2020 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-31840950

RESUMO

Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding, making it difficult for scientists to reveal the genetic regulatory mechanisms. Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions. It can identify interactions among target loci and all other loci in a genome with low cost and high resolution. Here, we developed CaptureProbe, a user-friendly, graphical Java tool for the design of capture probes across a range of target sites or regions. Numerous parameters helped to achieve and optimize the designed probes. Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity. Hence, this program will help scientists conduct genome spatial interaction research. CaptureProbe and source code are available at https://sourceforge.net/projects/captureprobe/.


Assuntos
Cromossomos/genética , Sondas de DNA/genética , Genômica/métodos , Software , Animais , Humanos
18.
J Environ Sci (China) ; 86: 87-96, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31787193

RESUMO

Sedum alfredii Hance is a cadmium (Cd)/zinc (Zn) hyperaccumulator native to China. However, its relatively low biomass restricted the large-scale application for heavy metal contamination remediation. The chromosome set doubling of S. alfredii in vitro was achieved by 0.1%-0.2% (W/V) colchicine treatment. The plant DNA ploidy was analyzed by flow cytometry and chromosome set doubling plants (CSD) were identified based on the obvious different sharp peak. A tissue culture experiment with different Cd treated levels and a field trial with natural polluted mined soil were conducted to study the effects of chromosome doubling on plant biomass and Cd accumulation in shoots. The results suggested that S. alfredii is a mixoploid. Compared with the wild type plants (WT), CSD exhibited typical "gigas" characteristics in morphology including stem thickness, root hair production, number of leaves and size of stoma guard cell. Fresh weight and dry weight of CSD were increased to 1.62-2.03-fold and 2.26-3.25-fold of WT. And Cd content of CSD showed a 17.49%-42.82% increase and 59% increase under tissue culture and field condition, accordingly. In addition, the TF and in BCF of CSD were 2.37- and 1.59-fold of WT, respectively. These results proved that it is feasible to promote phytoextraction efficiency of S. alfredii in Cd contaminated soils through chromosomal engineering, which provides a novel approach for hyperaccumulator application in phytoremediation.


Assuntos
Biodegradação Ambiental , Cromossomos , Metais Pesados/metabolismo , Sedum/genética , Poluentes do Solo/metabolismo , China , Sedum/metabolismo
19.
PLoS One ; 14(12): e0226746, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31856256

RESUMO

Lebiasinidae is a small fish family composed by miniature to small-sized fishes with few cytogenetic data (most of them limited to descriptions of diploid chromosome numbers), thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing, the first cytogenetic data for the red spotted tetra, Copeina guttata, including the standard karyotype, C-banding, repetitive DNA mapping by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH), providing chromosomal patterns and novel insights into the karyotype differentiation of the family. Males and females share diploid chromosome number 2n = 42 and karyotype composed of 2 metacentric (m), 4 submetacentric (sm) and 36 subtelocentric to acrocentric (st-a) chromosomes. Blocks of constitutive heterochromatin were observed in the centromeric and interstitial regions of several chromosomes, in addition to a remarkably large distal block, heteromorphic in size, which fully corresponded with the 18S rDNA sites in the fourth chromosomal pair. This overlap was confirmed by 5S/18S rDNA dual-color FISH. On the other hand, 5S rDNA clusters were situated in the long and short arms of the 2nd and 15th pairs, respectively. No sex-linked karyotype differences were revealed by male/female CGH experiments. The genomic probes from other two lebiasinid species, Lebiasina melanoguttata and Pyrrhulina brevis, showed positive hybridization signals only in the NOR region in the genome of C. guttata. We demonstrated that karyotype diversification in lebiasinids was accompanied by a series of structural and numeric chromosome rearrangements of different types, including particularly fusions and fissions.


Assuntos
Caraciformes/genética , Cariótipo , Filogenia , Animais , Caraciformes/classificação , Cromossomos/genética , Evolução Molecular , Feminino , Masculino , RNA Ribossômico/genética
20.
Cytogenet Genome Res ; 159(4): 208-214, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31846969

RESUMO

The karyotypes and other chromosomal markers of 4 catfish species, namely Lasiancistrus schomburgkii, Lasiancistrus sp., Araichthysloro, and Megalancistrus sp., members of a taxonomically complex and speciose tribe of catfishes Ancistrini, Hypostominae, were examined using conventional (Giemsa staining, Ag-NOR, and C-banding) and molecular cytogenetic protocols (FISH) and DNA barcoding. In L. schomburgkii, Lasiancistrus sp., and A.loro a diploid number 2n = 54 was observed, with karyotypes composed of 28m + 16sm + 10st, 36m + 12sm + 6st chromosomes, while Megalancistrus sp. had 2n = 52, with the karyotype composed of 28m + 16sm + 8st chromosomes. The Ag-NOR phenotypes were simple in all 4 species, which was confirmed by FISH with an 18S rDNA probe. However, the positive 5S rDNA sites varied among species: 2 chromosome pairs in L. schomburgkii, Lasiancistrus sp., and A. loro, and only 1 pair in Megalancistrus sp. The blocks of constitutive heterochromatin were poorly visible in the pericentromeric and telomeric regions of most chromosomes of the examined species by C-banding. The genetic distance analysis, based on mtDNA COI gene sequences (DNA barcoding), confirmed the species as 4 taxonomic units. Ours and other published data indicate that karyotype differentiation among Ancistrini is complex and divergent and indicates the occurrence of common chromosomal rearrangements, such as pericentric inversions conserving the diploid number, and other rearrangements that are more frequent in some genera, such as centric fusions in Ancistrus.


Assuntos
Peixes-Gato/genética , Animais , Inversão Cromossômica/genética , Cromossomos/genética , Citogenética/métodos , DNA Ribossômico/genética , Diploide , Feminino , Heterocromatina/genética , Cariótipo , Masculino , Filogenia , Telômero/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA