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1.
Dev Cell ; 57(8): 945-946, 2022 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-35472320

RESUMO

Mammalian cardiomyocytes (CMs) undergo polyploidization after birth, accompanied by the loss of CM proliferation and regenerative capacity, although why this occurs is still poorly understood. In this issue of Developmental Cell, Gan et al. show that premature CM polyploidization, through defective RNA splicing, is detrimental to ventricular wall growth.


Assuntos
Microtúbulos , Miócitos Cardíacos , Animais , Mamíferos , Miócitos Cardíacos/metabolismo , Ploidias , Splicing de RNA/genética
2.
PLoS One ; 17(4): e0267496, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35482804

RESUMO

Pelargonium is a versatile genus mainly from the Cape Region, South Africa. The genus is divided into four subgenera and 16 sections characterized by several groups of chromosomes sizes and numbers. The DNA content of species from all subgenera and sections of Pelargonium, except for the sections Subsucculentia and Campylia was estimated using flow cytometry. Nuclei of Pelargonium samples (leaf or petal tissue) and an internal plant standard (leaf tissue) were isolated together and stained with propidium iodide. The DNA content was estimated providing that the 2C peaks of sample and standard be in linearity in the flow cytometer histograms. In total, 96 Pelargonium accessions of 60 species (22 Pelargonium species for the first time) were analyzed. The 2C DNA content ranged from 0.84 pg (P. longifolium, section Hoarea) to 6.69 pg (P. schizopetalum, section Magnistipulacea) and the corresponding 1Cx DNA content from 0.42 pg (P. longifolium) to 1.72 pg (P. transvaalense. This demonstrates the high plasticity within the genus Pelargonium. Some species, such as P. peltatum accessions revealed a pronounced endopolyploidization in leaves but not in petals underlining the importance to choose the right tissue as sample for the flow cytometry analysis. The reported genome sizes are a step forward towards the characterization of the Pelargonium collection within the German Gene Bank for Ornamental Plants and a valuable base for future sequencing programs of the Pelargonium genomes.


Assuntos
Pelargonium , DNA de Plantas/análise , DNA de Plantas/genética , Citometria de Fluxo , Genoma de Planta , Pelargonium/genética , Ploidias
3.
Genes (Basel) ; 13(3)2022 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-35327971

RESUMO

The twenty-first century has been an era of extensive genome exploration and modifications, using advanced methods such as genome sequencing and editing [...].


Assuntos
DNA , Ploidias , DNA/genética , Citometria de Fluxo , Fungos/genética , Microscopia de Fluorescência , Plantas/genética
4.
PLoS One ; 17(3): e0265405, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35294505

RESUMO

Asparagus wild relatives could be a promising possibility to extent the genetic variability of garden asparagus and for new cultivars with favorable traits such as high yield stability, disease resistance and stress tolerance. In order to achieve an efficient use in breeding, a detailed cytogenetic characterization of the accessions is necessary. This study worked on 35 Asparagus accessions, including A. officinalis cultivars ('Darlise', 'Ravel' and 'Steiners Violetta') and Asparagus wild relatives, for which the number of chromosomes, their size, the nuclear DNA content, and the genomic distribution of 5S and 45S rDNA were analyzed. Different ploidy levels (diploid, triploid, tetraploid, pentaploid and hexaploid) were found. Furthermore, the size of the chromosomes of all diploid Asparagus accessions was determined which led to differences in the karyotypic formula. A. plocamoides harbors the smallest chromosome with 1.21 µm, whereas the largest chromosome with 5.43 µm was found in A. officinalis. In all accessions one 5S rDNA locus per genome was observed, while the number of 45S rDNA loci varied between one (A. albus, A. plumosus, A. stipularis) to four (A. setaceus). In most Asparagus accessions, the 5S and 45S rDNA signals were located on different chromosomes. In contrast, the genomes of A. africanus, A. plocamoides, A. sp. (a taxonomically unclassified Asparagus species from Asia) and A. verticillatus (diploid accessions) have one 5S and one 45S rDNA signal on the same chromosome. The measured 2C DNA content ranges from 1.43 pg (A. plocamoides, diploid) to 8.24 pg (A. amarus, hexaploid). Intraspecific variations for chromosome number, karyotypic formula, signal pattern with 5S and 45s rDNA probes and DNA content were observed. Interspecific variations were also recognized in the genus Asparagus.


Assuntos
Cromossomos de Plantas , Melhoramento Vegetal , Cromossomos de Plantas/genética , DNA Ribossômico/genética , Hibridização in Situ Fluorescente , Ploidias , RNA Ribossômico 5S/genética
5.
Dokl Biochem Biophys ; 502(1): 10-14, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35275299

RESUMO

For the first time, the composition and the content of the main components of the phenolic complex of aboveground organs of buckwheat plants (Fagopyrum esculentum Moench) with different levels of ploidy (2n and 4n) at the initial stages of ontogenesis and their changes under the action of cadmium (Cd, 65 µM) were studied by the method of high-performance liquid chromatography. In all variants, phenolic compounds (PCs) were represented by chlorogenic acid (phenylpropanoid), rutin (flavonol), as well as orientin, isoorientin, vitexin, and isovitexin (flavones). The amount of PCs in the cotyledon leaves in most cases exceeded that in the hypocotyls. Buckwheat seedlings of the tetraploid genotype are characterized by a higher accumulation of PCs as compared to the diploid genotype. Under the effect of Cd, the content of their individual representatives changed: in the hypocotyls of the diploid genotype, it decreased in most cases, whereas in the hypocotyls of the tetraploid genotype it increased. In the cotyledon leaves, the tendency was opposite. It was found that seedlings of two F. esculentum genotypes with different ploidy levels differed in the content of the main PCs and in their response to Cd, which is important for breeding this culture for stress resistance.


Assuntos
Fagopyrum , Cádmio/análise , Cádmio/farmacologia , Fagopyrum/química , Fagopyrum/genética , Fenóis , Ploidias , Plântula/genética
6.
Bull Exp Biol Med ; 172(5): 598-601, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35352248

RESUMO

Amyloidosis was modeled in young mice by administration of aqueous solution of soy cream substitute and then, amyloidogenesis was corrected by oral administration of dry red wine. In mice with amyloidosis, the area of megakaryocytes decreased by 1.69 times, the relative content of oxyphilic forms of megakaryocytes increased by 4.33 times, and ploidy did not change in comparison with the corresponding parameters in intact mice. Administration of red dry grape wine against the background of formation of systemic amyloidosis changed the reaction of megakaryocytes: the content of polychromatophilic forms was comparable to the level of intact control, the content of oxyphilic forms decreased by 3.11 times, the RNA and DNA content in megakaryocyte nuclei decreased proportionally, and the ploidy decreased. Thus, red grape wine reduced the response of the megakaryocyte genome to the external supply of amyloidogenic substance.


Assuntos
Amiloidose , Vinho , Animais , Megacariócitos , Camundongos , Camundongos Endogâmicos C57BL , Ploidias , Baço
7.
Am J Bot ; 109(2): 259-271, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35137947

RESUMO

PREMISE: Endoreduplication, nonheritable duplication of a nuclear genome, is widespread in plants and plays a role in developmental processes related to cell differentiation. However, neither ecological nor cytological factors influencing intraspecific variation in endoreduplication are fully understood. METHODS: We cultivated plants covering the range-wide natural diversity of diploid and tetraploid populations of Arabidopsis arenosa in common conditions to investigate the effect of original ploidy level on endoreduplication. We also raised plants from several foothill and alpine populations from different lineages and of both ploidies to test for the effect of elevation. We determined the endoreduplication level in leaves of young plants by flow cytometry. Using RNA-seq data available for our populations, we analyzed gene expression analysis in individuals that differed in endoreduplication level. RESULTS: We found intraspecific variation in endoreduplication that was mainly driven by the original ploidy level of populations, with significantly higher endoreduplication in diploids. An effect of elevation was also found within each ploidy, yet its direction exhibited rather regional-specific patterns. Transcriptomic analysis comparing individuals with high vs. low endopolyploidy revealed a majority of differentially expressed genes related to the stress and hormone response and to modifications especially in the cell wall and in chloroplasts. CONCLUSIONS: Our results support the general assumption of higher potential of low-ploidy organisms to undergo endoreduplication and suggest that endoreduplication is further integrated within the stress response pathways for a fine-tune adjustment of the endoreduplication process to their local environment.


Assuntos
Arabidopsis , Arabidopsis/genética , Diploide , Endorreduplicação/genética , Ploidias , Tetraploidia
8.
Funct Plant Biol ; 49(4): 333-350, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35190024

RESUMO

Severe water stress is responsible for reducing plant growth and reproduction. This study aimed to evaluate the physiological and biochemical mechanisms associated with the tolerance of two genotipes of bahiagrass (Paspalum notatum Flügge) with different ploidy level to water deficit and flooding at the reproductive stage. Photosynthetic performance of diploid and tetraploid plants was not affected by flooding. In contrast, the water deficit decreased stomatal conductance, increased leaf temperature, and resulted in a decrease in the assimilation rate of the two genotypes. Despite the greater activities of antioxidant enzymes, flooded roots accumulated hydrogen peroxide and malondialdehyde. Roots of plants exposed to water deficit maintained an accumulation of biomass similar to that of control plants; however, with higher levels of total phenol content, total soluble sugars and proline. Diploid plants subjected to flooding had more inflorescences, however, the drought reduced the total number of filled florets per plant. Less starch degradation allows the maintenance and recovery of biomass in the tetraploid genotype, which allows it to maintain its reproductive performance even under drought conditions. Overall, the synthesis of osmoprotectants and activation of antioxidant machinery are important strategies in the tolerance of bahiagrass to water stress at the reproductive stage.


Assuntos
Secas , Paspalum , Genótipo , Paspalum/genética , Ploidias , Reprodução
9.
PLoS One ; 17(1): e0261742, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34995300

RESUMO

Extreme weather and globalisation leave our climate vulnerable to invasion by alien species, which have negative impacts on the economy, biodiversity, and ecosystem services. Rapid and accurate identification is key to the control of invasive alien species. However, visually similar species hinder conservation efforts, for example hybrids within the Japanese Knotweed complex.We applied the novel method of ATR-FTIR spectroscopy combined with chemometrics (mathematics applied to chemical data) to historic herbarium samples, taking 1580 spectra in total. Samples included five species from within the interbreeding Japanese Knotweed complex (including three varieties of Japanese Knotweed), six hybrids and five species from the wider Polygonaceae family. Spectral data from herbarium specimens were analysed with several chemometric techniques: support vector machines (SVM) for differentiation between plant types, supported by ploidy levels; principal component analysis loadings and spectral biomarkers to explore differences between the highly invasive Reynoutria japonica var. japonica and its non-invasive counterpart Reynoutria japonica var. compacta; hierarchical cluster analysis (HCA) to investigate the relationship between plants within the Polygonaceae family, of the Fallopia, Reynoutria, Rumex and Fagopyrum genera.ATR-FTIR spectroscopy coupled with SVM successfully differentiated between plant type, leaf surface and geographical location, even in herbarium samples of varying age. Differences between Reynoutria japonica var. japonica and Reynoutria japonica var. compacta included the presence of two polysaccharides, glucomannan and xyloglucan, at higher concentrations in Reynoutria japonica var. japonica than Reynoutria japonica var. compacta. HCA analysis indicated that potential genetic linkages are sometimes masked by environmental factors; an effect that can either be reduced or encouraged by altering the input parameters. Entering the absorbance values for key wavenumbers, previously highlighted by principal component analysis loadings, favours linkages in the resultant HCA dendrogram corresponding to expected genetic relationships, whilst environmental associations are encouraged using the spectral fingerprint region.The ability to distinguish between closely related interbreeding species and hybrids, based on their spectral signature, raises the possibility of using this approach for determining the origin of Japanese knotweed infestations in legal cases where the clonal nature of plants currently makes this difficult and for the targeted control of species and hybrids. These techniques also provide a new method for supporting biogeographical studies.


Assuntos
Espécies Introduzidas , Ploidias , Polygonaceae/classificação , Polygonaceae/crescimento & desenvolvimento , Polygonaceae/genética , Espectroscopia de Infravermelho com Transformada de Fourier
10.
Cells ; 11(1)2022 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-35011735

RESUMO

The myocardium of children with tetralogy of Fallot (TF) undergoes hemodynamic overload and hypoxemia immediately after birth. Comparative analysis of changes in the ploidy and morphology of the right ventricular cardiomyocytes in children with TF in the first years of life demonstrated their significant increase compared with the control group. In children with TF, there was a predominantly diffuse distribution of Connexin43-containing gap junctions over the cardiomyocytes sarcolemma, which redistributed into the intercalated discs as cardiomyocytes differentiation increased. The number of Ki67-positive cardiomyocytes varied greatly and amounted to 7.0-1025.5/106 cardiomyocytes and also were decreased with increased myocytes differentiation. Ultrastructural signs of immaturity and proliferative activity of cardiomyocytes in children with TF were demonstrated. The proportion of interstitial tissue did not differ significantly from the control group. The myocardium of children with TF under six months of age was most sensitive to hypoxemia, it was manifested by a delay in the intercalated discs and myofibril assembly and the appearance of ultrastructural signs of dystrophic changes in the cardiomyocytes. Thus, the acceleration of ontogenetic growth and differentiation of the cardiomyocytes, but not the reactivation of their proliferation, was an adaptation of the immature myocardium of children with TF to hemodynamic overload and hypoxemia.


Assuntos
Diferenciação Celular , Ventrículos do Coração/patologia , Miócitos Cardíacos/patologia , Ploidias , Tetralogia de Fallot/patologia , Estudos de Casos e Controles , Proliferação de Células , Tamanho Celular , Criança , Pré-Escolar , Conexina 43/metabolismo , Feminino , Junções Comunicantes/metabolismo , Junções Comunicantes/ultraestrutura , Humanos , Lactente , Antígeno Ki-67/metabolismo , Masculino , Miocárdio/patologia , Miocárdio/ultraestrutura , Miócitos Cardíacos/ultraestrutura
11.
Int J Mol Sci ; 23(1)2022 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-35008920

RESUMO

The objective of the present research was to study the effect of cold shock (3 °C and 6 °C) on fertilized eggs of the sterlet, Acipenser ruthenus L. Cold shock was applied for various durations (30, 60 and 90 min) and the ploidy levels, survival, and genotypes of the treated embryos/larvae were recorded. Analysis of ploidy levels confirmed the presence of diploid, triploid, and mosaic (1n/2n, 2n/3n, and 1n/2n/3n) genotypes in experimental groups, while it was strictly diploid in control groups. Microsatellite genotyping confirmed both the incidence of polyspermy and retention of the 2nd polar body in experimental groups. However, patterns of inheritance in all diploid offspring in experimental and control groups revealed classical Mendelian disomic inheritance. Interestingly, the observed mosaic sterlets had normal morphology and were alive. However, some larvae had abnormal morphology which may be due to haploid syndrome. In all treatment groups (treatments: 3 °C-30 min; 3 °C-60 min; 3 °C-90 min; 6 °C-60 min), where the percentage of polyploid/mosaic larvae were high, the mortality was also high. Whereas, in the control groups (where there were only diploid (2n) larvae), the mortality was relatively low.


Assuntos
Resposta ao Choque Frio/fisiologia , Peixes/crescimento & desenvolvimento , Peixes/genética , Ploidias , Alelos , Animais , Segregação de Cromossomos , Desenvolvimento Embrionário , Peixes/embriologia , Larva/crescimento & desenvolvimento , Repetições de Microssatélites/genética , Análise de Sobrevida
12.
Gastroenterology ; 162(1): 238-252, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34481846

RESUMO

BACKGROUND & AIMS: Copy number alterations (CNAs), elicited by genome instability, are a major source of intratumor heterogeneity. How CNAs evolve in hepatocellular carcinoma (HCC) remains unknown. METHODS: We performed single-cell DNA sequencing (scDNA-seq) on 1275 cells isolated from 10 patients with HCC, ploidy-resolved scDNA-seq on 356 cells from 1 additional patient, and single-cell RNA sequencing on 27,344 cells from 3 additional patients. Three statistical fitting models were compared to investigate the CNA accumulation pattern. RESULTS: Cells in the tumor were categorized into the following 3 subpopulations: euploid, pseudoeuploid, and aneuploid. Our scDNA-seq analysis revealed that CNA accumulation followed a dual-phase copy number evolution model, that is, a punctuated phase followed by a gradual phase. Patients who exhibited prolonged gradual phase showed higher intratumor heterogeneity and worse disease-free survival. Integrating bulk RNA sequencing of 17 patients with HCC, published datasets of 1196 liver tumors, and immunohistochemical staining of 202 HCC tumors, we found that high expression of CAD, a gene involved in pyrimidine synthesis, was correlated with rapid tumorigenesis and reduced survival. The dual-phase copy number evolution model was validated by our single-cell RNA sequencing data and published scDNA-seq datasets of other cancer types. Furthermore, ploidy-resolved scDNA-seq revealed the common clonal origin of diploid- and polyploid-aneuploid cells, suggesting that polyploid tumor cells were generated by whole genome doubling of diploid tumor cells. CONCLUSIONS: Our work revealed a novel dual-phase copy number evolution model, showed HCC with longer gradual phase was more severe, identified CAD as a promising biomarker for early recurrence of HCC, and supported the diploid origin of polyploid HCC.


Assuntos
Biomarcadores Tumorais/genética , Carcinoma Hepatocelular/genética , Evolução Clonal , Heterogeneidade Genética , Neoplasias Hepáticas/genética , Análise de Sequência de DNA , Análise de Célula Única , Adulto , Idoso , Carcinoma Hepatocelular/metabolismo , Variações do Número de Cópias de DNA , Progressão da Doença , Intervalo Livre de Doença , Feminino , Dosagem de Genes , Regulação Neoplásica da Expressão Gênica , Instabilidade Genômica , Humanos , Neoplasias Hepáticas/mortalidade , Neoplasias Hepáticas/patologia , Neoplasias Hepáticas/terapia , Masculino , Pessoa de Meia-Idade , Modelos Genéticos , Recidiva Local de Neoplasia , Ploidias , Fatores de Tempo
13.
Am J Pathol ; 192(1): 56-71, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34599880

RESUMO

N6-methyladenosine (m6A), the most abundant internal modifier of mRNAs installed by the methyltransferase 13 (METTL3) at the (G/A)(m6A)C motif, plays a critical role in the regulation of gene expression. METTL3 is essential for embryonic development, and its dysregulation is linked to various diseases. However, the role of METTL3 in liver biology is largely unknown. In this study, METTL3 function was unraveled in mice depleted of Mettl3 in neonatal livers (Mettl3fl/fl; Alb-Cre). Liver-specific Mettl3 knockout (M3LKO) mice exhibited global decrease in m6A on polyadenylated RNAs and pathologic features associated with nonalcoholic fatty liver disease (eg, hepatocyte ballooning, ductular reaction, microsteatosis, pleomorphic nuclei, DNA damage, foci of altered hepatocytes, focal lobular and portal inflammation, and elevated serum alanine transaminase/alkaline phosphatase levels). Mettl3-depleted hepatocytes were highly proliferative, with decreased numbers of binucleate hepatocytes and increased nuclear polyploidy. M3LKO livers were characterized by reduced m6A and expression of several key metabolic transcripts regulated by circadian rhythm and decreased nuclear protein levels of the core clock transcription factors BMAL1 and CLOCK. A significant decrease in total Bmal1 and Clock mRNAs but an increase in their nuclear levels were observed in M3LKO livers, suggesting impaired nuclear export. Consistent with the phenotype, methylated (m6A) RNA immunoprecipitation coupled with sequencing and RNA sequencing revealed transcriptome-wide loss of m6A markers and alterations in abundance of mRNAs involved in metabolism in M3LKO. Collectively, METTL3 and m6A modifications are critical regulators of liver homeostasis and function.


Assuntos
Ritmo Circadiano/genética , Regulação da Expressão Gênica , Hepatócitos/metabolismo , Homeostase , Fígado/metabolismo , Metiltransferases/metabolismo , Ploidias , Fatores de Transcrição ARNTL/metabolismo , Animais , Animais Recém-Nascidos , Sequência de Bases , Proteínas CLOCK/genética , Proteínas CLOCK/metabolismo , Proteínas de Ciclo Celular/metabolismo , Núcleo Celular/metabolismo , Metilação de DNA/genética , Deleção de Genes , Perfilação da Expressão Gênica , Fígado/patologia , Camundongos Knockout , Poliadenilação , Poliploidia , Proteínas Tirosina Quinases/metabolismo , Transcriptoma/genética
14.
J Appl Genet ; 63(2): 199-211, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-34859368

RESUMO

Caladium × hortulanum 'Fancy' is an important ornamental plant grown in pots and landscapes and known for its colorful leaves often used for interior decorations. In this work, we present a method of in vitro regeneration from three explants source through direct somatic embryogenesis (DSE) wherein the regenerated plants were screened for ploidy changes through flow cytometry analysis. Tuber, leaf and petiole explants were cultured on MS basal medium supplemented with 1-napthalene acetic acid (NAA), 6-benzyl amino purine (BAP) and N-phenyl-N'-1, 2,3-thiadiazol-5-ylurea (TDZ) concentrations. Tuber explants induced highest direct somatic embryos on NAA (1 mg L- 1) + BAP (0.5 mg L- 1) with 55.6 mean number of embryos per explant while as leaf and petiole explants amended with 1 mg L- 1 TDZ developed 18.7 and 12.27 mean number of embryos per explant respectively. The highest embryo conversion frequency was achieved on BAP (2 mg L- 1) + NAA (0.2 mg L- 1) with 44.2, 18.7 and 7.5 mean number of plantlets produced per tuber, leaf and petiole explant respectively after 4 weeks of culture. Plantlets were later rooted and maximum number of roots (6.33) per shoot was achieved on 2 mg L- 1 indolebutyric acid amended medium. Description of the process of DSE is presented through the histological and SEM evidences. The 2C DNA content of field grown plants and the DSE regenerants evaluated under flow cytometric analysis were 8.06 pg and 8.28 pg respectively showing no ploidy changes. Hence, a successful protocol of inducing direct somatic embryos from three explant types with efficient embryo conversion frequency was obtained with regenerants showing similar DNA ploidy as that of their parent plants.


Assuntos
Ploidias , Regeneração , Desenvolvimento Embrionário , Citometria de Fluxo , Folhas de Planta/genética , Regeneração/genética
15.
Zygote ; 30(1): 25-39, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-34275512

RESUMO

Embryos undergo chaotic division and decrease in quality on day 3 with a reduction in the rates of subsequent blastocyst formation. Disordered cleavage causes a deterioration in embryonic quality, here we assessed the relationship between an cleavage model in first mitosis and the chromosomal status of human embryos, and discuss the potential biological and clinical implications for the cleavage model as a single parameter that can be used to assess embryonic quality. Thirty-two infertile couples, with normal karyotypes and who underwent their first IVF cycle were recruited to donate one normal two-cell-stage embryo each for this study between 2019 and 2020. Twenty-eight two-cell embryos underwent preimplantation genetic testing of each blastomere, and four chaotic-division embryos were stained with Hoechst and cultured in a confocal laser-scanning microscopy incubator system. This system showed high specificity and PPV but low sensitivity and NPV using the CM in the prediction of euploidy, indicating that CM could be considered a screening method for embryo selection; additional observational studies using the CM to select transferable embryos are needed before it can be used in clinical practice.


Assuntos
Blastômeros , Diagnóstico Pré-Implantação , Blastocisto , Feminino , Fertilização In Vitro , Humanos , Mosaicismo , Ploidias , Gravidez
16.
Mol Ecol Resour ; 22(1): 254-271, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34310066

RESUMO

Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within-species studies based on high-resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0-23.7 Gb. We assembled 25,677 high-quality transcripts with an average length of 1,333 bp based on deep RNA-sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High-quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.


Assuntos
Gleiquênias , Polimorfismo de Nucleotídeo Único , Transcriptoma , Ecossistema , Gleiquênias/genética , Genética Populacional , Ploidias , Suíça
17.
Genome ; 65(4): 219-227, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-34855521

RESUMO

The avian pectoralis muscle demonstrates plasticity with regard to size, so that temperate birds facing winter conditions or birds enduring a migration bout tend to have significant increases in the size and mass of this tissue due to muscular hypertrophy. Myonuclear domain (MND), the volume of cytoplasm a myonuclei services, in the pectoralis muscle of birds seems to be altered during thermal stress or changing seasons. However, there is no information available regarding muscle DNA content or ploidy level within the avian pectoralis. Changes in muscle DNA content can be used in this tissue to aid in size and mass changes. Here, we hypothesized that long-distance migrants or temperate residents would use the process of endoreduplication to aid in altering muscle size. Mostly contradictory to our hypotheses, we found no differences in the mean muscle DNA content in any of the 62 species of birds examined in this study. We also found no correlations between mean muscle DNA content and other muscle structural measurements, such as the number of nuclei per millimeter of fiber, myonuclear domain, and fiber cross-sectional area. Thus, while avian muscle seems more phenotypically plastic than mammalian muscle, the biological processes surrounding myonuclear function may be more closely related to those seen in mammals.


Assuntos
Núcleo Celular , Fibras Musculares Esqueléticas , Animais , Aves/genética , Núcleo Celular/genética , DNA , Mamíferos , Fibras Musculares Esqueléticas/fisiologia , Músculos Peitorais , Ploidias
18.
Mol Diagn Ther ; 26(1): 105-116, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34932189

RESUMO

BACKGROUND AND OBJECTIVE: Human epidermal growth factor receptor 2 (HER2) protein overexpression is one of the most significant biomarkers for breast cancer diagnostics, treatment prediction, and prognostics. The high accessibility of HER2 inhibitors in routine clinical practice directly translates into the diagnostic need for precise and robust marker identification. Even though multigene next-generation sequencing methodologies have slowly taken over the field of single-biomarker molecular tests, the copy number alterations such as amplification of the HER2-coding ERBB2 gene are hard to validate on next-generation sequencing platforms as they are characterized by chromosomal structural heterogeneity, polysomy, and genomic context of ploidy. In our study, we tested the approach of using whole genome sequencing instead of next-generation sequencing panels to determine HER2 status in the clinical set-up. METHODS: We used a large dataset of 876 patients with breast cancer whole genomes with curated clinical data and an additional set of 551 patients' external genomic data. We used the decision-tree-based algorithm for optimization of the diagnostic tool for HER2 status assessment by whole genome sequencing. RESULTS: The most efficient approach to assess HER2 status in whole genome sequencing data was the ploidy-corrected copy number, utilizing ERBB2 copy number and mean tumor ploidy. The classifier achieved sensitivity of 91.18% and specificity of 98.69% on the internal validation dataset and 89.86% and 96.06% on the external data, which is similar to other next-generation sequencing methods, currently tested in the clinic. CONCLUSIONS: We provide evidence that the HER2 status may be reliably determined by whole genome sequencing and is applicable across different laboratory protocols and pipelines. We suggest using the ploidy-corrected copy number for diagnostic purposes.


Assuntos
Neoplasias da Mama , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Variações do Número de Cópias de DNA , Feminino , Genes erbB-2 , Humanos , Ploidias , Receptor ErbB-2/genética , Sequenciamento Completo do Genoma
19.
Mol Phylogenet Evol ; 166: 107332, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34687842

RESUMO

Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western North American Isoëtes, to understand the role of hybridization and high-level polyploidy in generating and maintaining novel diversity. To uncover these processes, we use restriction-site associated DNA sequencing (RADseq), multiple alleles of a single low-copy nuclear marker, whole plastomes, cytology (genome size estimates and chromosome counts), and reproductive status (fertile or sterile). With this dataset, we show that hybridization occurs easily between species in this complex and is bidirectional between identical, but not different, cytotypes. Furthermore, we show that fertile allopolyploids appear to have formed repeatedly from sterile homoploid and interploid hybrids. We propose that low prezygotic reproductive barriers and a high frequency of whole-genome duplication allow for high-level polyploid systems to generate novel lineages, and that these mechanisms may be important in shaping extant Isoëtes diversity.


Assuntos
Ploidias , Poliploidia , Tamanho do Genoma , Humanos , América do Norte , Filogenia
20.
Fish Shellfish Immunol ; 120: 547-559, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34923115

RESUMO

Aeromonas hydrophila can pose a great threat to survival of freshwater fish. In this study, A. hydrophila infection could decrease blood cell numbers, promote blood cell damage as well as alter the levels of alkaline phosphatase (ALP), lysozyme (LZM), aspartate aminotransferase (AST), total antioxidant capacity (T-AOC), total superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) in immune-related tissues of red crucian carp (RCC, 2 N = 100) and triploid cyprinid fish (3 N fish, 3 N = 150). In addition, the significant alternation of antioxidant status was observed in PBMCs isolated from RCC and 3 N following LPS stimulation. The core differential expression genes (DEGs) involved in apoptosis, immunity, inflammation and cellular signals were co-expressed differentially in RCC and 3 N following A. hydrophila challenge. NOD-like receptor (NLR) signals appeared to play a critical role in A. hydrophila-infected fish. DEGs of NLR signals in RCCah vs RCCctl were enriched in caspase-1-dependent Interleukin-1ß (IL-1ß) secretion, interferon (IFN) signals as well as cytokine activation, while DEGs of NLR signals in 3Nah vs 3Nctl were enriched in caspase-1-dependent IL-1ß secretion and antibacterial autophagy. These results highlighted the differential signal regulation of different ploidy cyprinid fish to cope with bacterial infection.


Assuntos
Carpas , Doenças dos Peixes , Infecções por Bactérias Gram-Negativas , Transcriptoma , Aeromonas hydrophila , Animais , Antioxidantes , Células Sanguíneas , Carpas/genética , Carpas/imunologia , Caspases , Suplementos Nutricionais , Resistência à Doença , Doenças dos Peixes/imunologia , Doenças dos Peixes/microbiologia , Proteínas de Peixes/genética , Perfilação da Expressão Gênica , Infecções por Bactérias Gram-Negativas/imunologia , Infecções por Bactérias Gram-Negativas/veterinária , Imunidade Inata , Ploidias
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