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1.
Heredity (Edinb) ; 133(4): 227-237, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-39090316

RESUMO

How frequently hybridisation and gene flow occur in the contact zones of diverging taxa is important for understanding the speciation process. Stigmaeopsis sabelisi and Stigmaeopsis miscanthi high-aggression form (hereafter, S. miscanthi HG) are haplodiploid, social spider mites that infest the Chinese silver grass, Miscanthus sinensis. These two species are closely related and parapatrically distributed in Japan. In mountainous areas, S. sabelisi and S. miscanthi HG are often found in the highlands and lowlands, respectively, suggesting that they are in contact at intermediate altitudes. It is estimated that they diverged from their common ancestors distributed in subtropical regions (south of Japan) during the last glacial period, expanded their distribution into the Japanese Archipelago, and came to have such a parapatric distribution (secondary contact). As their reproductive isolation is strong but incomplete, hybridisation and genetic introgression are expected at their distributional boundaries. In this study, we investigated their spatial distribution patterns along the elevation on Mt. Amagi using male morphological differences, and investigated their hybridisation status using single-nucleotide polymorphisms by MIG-seq. We found their contact zone at altitudes of 150-430 m, suggesting that their contact zone is prevalent in the parapatric area, which is in line with a previous study. Interspecific mating was predicted based on the sex ratio in the contact zone. No obvious hybrids were found, but genetic introgression was detected although it was extremely low.


Assuntos
Introgressão Genética , Hibridização Genética , Polimorfismo de Nucleotídeo Único , Tetranychidae , Animais , Tetranychidae/genética , Masculino , Fluxo Gênico , Japão , Haploidia , Isolamento Reprodutivo , Genética Populacional , Especiação Genética , Diploide , Feminino
2.
Nat Commun ; 15(1): 6956, 2024 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-39138168

RESUMO

Structural variants (SVs) significantly contribute to human genome diversity and play a crucial role in precision medicine. Although advancements in single-molecule long-read sequencing offer a groundbreaking resource for SV detection, identifying SV breakpoints and sequences accurately and robustly remains challenging. We introduce VolcanoSV, an innovative hybrid SV detection pipeline that utilizes both a reference genome and local de novo assembly to generate a phased diploid assembly. VolcanoSV uses phased SNPs and unique k-mer similarity analysis, enabling precise haplotype-resolved SV discovery. VolcanoSV is adept at constructing comprehensive genetic maps encompassing SNPs, small indels, and all types of SVs, making it well-suited for human genomics studies. Our extensive experiments demonstrate that VolcanoSV surpasses state-of-the-art assembly-based tools in the detection of insertion and deletion SVs, exhibiting superior recall, precision, F1 scores, and genotype accuracy across a diverse range of datasets, including low-coverage (10x) datasets. VolcanoSV outperforms assembly-based tools in the identification of complex SVs, including translocations, duplications, and inversions, in both simulated and real cancer data. Moreover, VolcanoSV is robust to various evaluation parameters and accurately identifies breakpoints and SV sequences.


Assuntos
Diploide , Genoma Humano , Variação Estrutural do Genoma , Polimorfismo de Nucleotídeo Único , Humanos , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Software , Haplótipos
3.
Nat Genet ; 56(8): 1566-1573, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39103649

RESUMO

Telomere-to-telomere (T2T) assemblies reveal new insights into the structure and function of the previously 'invisible' parts of the genome and allow comparative analyses of complete genomes across entire clades. We present here an open collaborative effort, termed the 'Ruminant T2T Consortium' (RT2T), that aims to generate complete diploid assemblies for numerous species of the Artiodactyla suborder Ruminantia to examine chromosomal evolution in the context of natural selection and domestication of species used as livestock.


Assuntos
Ruminantes , Telômero , Telômero/genética , Animais , Ruminantes/genética , Evolução Molecular , Genoma/genética , Seleção Genética , Filogenia , Diploide
4.
Am J Bot ; 111(8): e16386, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39107998

RESUMO

PREMISE: A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. METHODS: Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange. RESULTS: We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species. CONCLUSIONS: Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0-0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.


Assuntos
Conversão Gênica , Gossypium , Filogenia , Poliploidia , Gossypium/genética , Genoma de Planta , Polimorfismo de Nucleotídeo Único , Diploide , Genes de Plantas , Cromossomos de Plantas/genética
5.
Nat Commun ; 15(1): 6893, 2024 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-39134553

RESUMO

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.


Assuntos
Cromossomos de Plantas , Evolução Molecular , Poliploidia , Salix , Cromossomos Sexuais , Cromossomos de Plantas/genética , Salix/genética , Cromossomos Sexuais/genética , Filogenia , Genoma de Planta , Diploide , Haplótipos
6.
G3 (Bethesda) ; 14(9)2024 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-39120426

RESUMO

Whole genome duplications are implicated in genome instability and tumorigenesis. Human and yeast polyploids exhibit increased replication stress and chromosomal instability, both hallmarks of cancer. In this study, we investigate the transcriptional response of Schizosaccharomyces pombe to increased ploidy generally, and in response to treatment with the genotoxin methyl methanesulfonate (MMS). We find that treatment of MMS induces upregulation of genes involved in general response to genotoxins, in addition to cell cycle regulatory genes. Downregulated genes are enriched in transport and sexual reproductive pathways. We find that the diploid response to MMS is muted compared to the haploid response, although the enriched pathways remain largely the same. Overall, our data suggests that the global S. pombe transcriptome doubles in response to increased ploidy but undergoes modest transcriptional changes in both unperturbed and genotoxic stress conditions.


Assuntos
Dano ao DNA , Diploide , Regulação Fúngica da Expressão Gênica , Haploidia , Schizosaccharomyces , Schizosaccharomyces/genética , Schizosaccharomyces/efeitos dos fármacos , Metanossulfonato de Metila/farmacologia , Transcriptoma , Transcrição Gênica , Perfilação da Expressão Gênica , Mutagênicos/toxicidade , Mutagênicos/farmacologia
7.
Am J Bot ; 111(8): e16387, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39113228

RESUMO

PREMISE: Whole-genome duplication (WGD, polyploidization) has been identified as a driver of genetic and phenotypic novelty, having pervasive consequences for the evolution of lineages. While polyploids are widespread, especially among plants, the long-term establishment of polyploids is exceedingly rare. Genome doubling commonly results in increased cell sizes and metabolic expenses, which may be sufficient to modulate polyploid establishment in environments where their diploid ancestors thrive. METHODS: We developed a mechanistic simulation model of photosynthetic individuals to test whether changes in size and metabolic efficiency allow autopolyploids to coexist with, or even invade, ancestral diploid populations. Central to the model is metabolic efficiency, which determines how energy obtained from size-dependent photosynthetic production is allocated to basal metabolism as opposed to somatic and reproductive growth. We expected neopolyploids to establish successfully if they have equal or higher metabolic efficiency as diploids or to adapt their life history to offset metabolic inefficiency. RESULTS: Polyploid invasion was observed across a wide range of metabolic efficiency differences between polyploids and diploids. Polyploids became established in diploid populations even when they had a lower metabolic efficiency, which was facilitated by recurrent formation. Competition for nutrients is a major driver of population dynamics in this model. Perenniality did not qualitatively affect the relative metabolic efficiency from which tetraploids tended to establish. CONCLUSIONS: Feedback between size-dependent metabolism and energy allocation generated size and age differences between plants with different ploidies. We demonstrated that even small changes in metabolic efficiency are sufficient for the establishment of polyploids.


Assuntos
Poliploidia , Modelos Biológicos , Evolução Biológica , Fotossíntese , Diploide , Características de História de Vida
8.
G3 (Bethesda) ; 14(8)2024 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-38954534

RESUMO

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximizes the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96-192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1,232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low false discovery rate (<0.01), and excellent specificity (0.96-0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents.


Assuntos
Diploide , Software , Triploidia , Animais , Polimorfismo de Nucleotídeo Único , Feminino , Genótipo , Alelos , Masculino
9.
Nat Commun ; 15(1): 5872, 2024 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-38997287

RESUMO

How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.


Assuntos
Diploide , Raízes de Plantas , Plantas Tolerantes a Sal , Raízes de Plantas/microbiologia , Plantas Tolerantes a Sal/microbiologia , Plantas Tolerantes a Sal/genética , Vigor Híbrido/genética , Filogenia , Genoma Fúngico , Ascomicetos/genética , Ascomicetos/metabolismo , Regulação Fúngica da Expressão Gênica , Endófitos/genética , Endófitos/metabolismo , Estresse Fisiológico/genética , Fenótipo , Tolerância ao Sal/genética , Hibridização Genética
10.
PLoS One ; 19(7): e0307023, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39024350

RESUMO

Polyploidy is thought to enable species diversification and adaptation to extreme environments. Resolving the ecological differences between a taxon's ploidy levels would therefore provide important insights into local adaptation and speciation. The genus Betula includes many polyploids, but estimates of their phylogenetic relationships and evolutionary history are uncertain because of cryptic lineages and species. As one of the southern boundary populations of Betula ermanii in Japan has been shown to have distinctive genetic characteristics and traits, the differences in ploidy levels between three southern boundary and various other Japanese B. ermanii populations were investigated using flow cytometry. Leaf and seed morphologies were also compared. Apart from individuals in southern boundary populations, all those sampled were tetraploid. Individuals from the southern boundary populations were mostly diploid, apart from a few from lower altitude Shikoku populations, which were tetraploid. Leaf and seed morphologies differed between tetraploids and diploids. Diploid individuals were characterized by leaves with a heart-shaped base and many leaf teeth, and seeds with relatively longer wings. The diploid populations could be considered a cryptic relict lineage of B. ermanii, and there is a possibility that this lineage is a diploid ancestor of B. ermanii and a relict population of the Sohayaki element. Further investigation of the Japanese Betula phylogenetic relationships would enable an informed discussion of taxonomic revisions.


Assuntos
Betula , Diploide , Filogenia , Japão , Betula/genética , Folhas de Planta/genética , Sementes/genética , Poliploidia
11.
Sci Rep ; 14(1): 15509, 2024 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-38969683

RESUMO

Polyploidization plays an important role in plant evolution and biodiversity. However, intraspecific polyploidy compared to interspecific polyploidy received less attention. Clintonia udensis (Liliaceae) possess diploid (2n = 2x = 14) and autotetraploid (2n = 4x = 28) cytotypes. In the Hualongshan Mountains, the autotetraploids grew on the northern slope, while the diploids grew on the southern slopes. The clonal growth characteristics and clonal architecture were measured and analyzed by field observations and morphological methods. The diversity level and differentiation patterns for two different cytotypes were investigated using SSR markers. The results showed that the clonal growth parameters, such as the bud numbers of each rhizome node and the ratio of rhizome branches in the autotetraploids were higher than those in the diploids. Both the diploids and autotetraploids appeared phalanx clonal architectures with short internodes between ramets. However, the ramets or genets of the diploids had a relatively scattered distribution, while those of the autotetraploids were relatively clumping. The diploids and autotetraploids all allocated more biomass to their vegetative growth. The diploids had a higher allocation to reproductive organs than that of autotetraploids, which indicated that the tetraploids invested more resources in clonal reproduction than diploids. The clone diversity and genetic diversity of the autotetraploids were higher than that of the diploids. Significant genetic differentiation between two different cytotypes was observed (P < 0.01). During establishment and evolution, C. udensis autotetraploids employed more clumping phalanx clonal architecture and exhibited more genetic variation than the diploids.


Assuntos
Diploide , Variação Genética , Tetraploidia , China , Biodiversidade , Repetições de Microssatélites/genética
12.
Plant J ; 119(5): 2236-2254, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38981008

RESUMO

The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR. Employing NGS-based HybSeq and RADSeq methodologies, flow cytometry, karyology, and ecological modeling, we scrutinize the intricacies of its polyploid evolution. Phylogenetic reconstructions using 951 low-copy nuclear genes confirm Pteronia as a well-supported, distinct clade within the tribe Astereae. The ingroup displays a structure indicative of rapid radiation likely antedating polyploid establishment, with the two main groups demarcated by their presence or absence in the fynbos biome. Genome size analysis encompasses 1293 individuals across 347 populations, elucidating significant variation ranging from 6.1 to 34.2 pg (2C-value). Pteronia demonstrates substantially large genome sizes within Astereae and phanerophytes. Polyploidy is identified in 31% of the studied species, with four discerned ploidy levels (2x, 4x, 6x, 8x). Cytotypes exhibit marked distinctions in environmental traits, influencing their distribution across biomes and augmenting their niche differentiation. These revelations challenge the presumed scarcity of polyploidy in the Cape flora, underscoring the imperative need for detailed population studies. The intricate evolutionary history of Pteronia, characterized by recent polyploidy and genome size variation, contributes substantially to the comprehension of diversification patterns within the GCFR biodiversity hotspot.


Assuntos
Asteraceae , Diploide , Genoma de Planta , Filogenia , Poliploidia , Genoma de Planta/genética , Asteraceae/genética , Tamanho do Genoma , Evolução Biológica , Biodiversidade , Evolução Molecular
13.
BMC Plant Biol ; 24(1): 492, 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38831289

RESUMO

Non-hydraulic root source signaling (nHRS) is a unique positive response to soil drying in the regulation of plant growth and development. However, it is unclear how the nHRS mediates the tradeoff between source and sink at the late growth stages and its adaptive mechanisms in primitive wheat. To address this issue, a root-splitting design was made by inserting solid partition in the middle of the pot culture to induce the occurrence of nHRS using four wheat cultivars (MO1 and MO4, diploid; DM22 and DM31, tetraploid) as materials. Three water treatments were designed as 1) both halves watered (CK), 2) holistic root system watered then droughted (FS), 3) one-half of the root system watered and half droughted (PS). FS and PS were designed to compare the role of the full root system and split root system to induce nHRS. Leaves samples were collected during booting and anthesis to compare the role of nHRS at both growth stages. The data indicated that under PS treatment, ABA concentration was significantly higher than FS and CK, demonstrating the induction of nHRS in split root design and nHRS decreased cytokinin (ZR) levels, particularly in the PS treatment. Soluble sugar and proline accumulation were higher in the anthesis stage as compared to the booting stage. POD activity was higher at anthesis, while CAT was higher at the booting stage. Increased ABA (nHRS) correlated with source-sink relationships and metabolic rate (i.e., leaf) connecting other stress signals. Biomass density showed superior resource acquisition and utilization capabilities in both FS and PS treatment as compared to CK in all plants. Our findings indicate that nHRS-induced alterations in phytohormones and their effect on source-sink relations were allied with the growth stages in primitive wheat.


Assuntos
Diploide , Raízes de Plantas , Transdução de Sinais , Tetraploidia , Triticum , Triticum/genética , Triticum/crescimento & desenvolvimento , Triticum/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/metabolismo , Raízes de Plantas/genética , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/metabolismo , Brotos de Planta/genética , Reguladores de Crescimento de Plantas/metabolismo , Ácido Abscísico/metabolismo , Citocininas/metabolismo , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/metabolismo , Folhas de Planta/genética
14.
BMC Genomics ; 25(1): 572, 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38844832

RESUMO

KNOXs, a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and abiotic stress in plants. However, the KNOX gene family has not been explored in sweet potato. In this study, through sequence alignment, genomic structure analysis, and phylogenetic characterization, 17, 12 and 11 KNOXs in sweet potato (I. batatas, 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30) were identified. The protein physicochemical properties, chromosome localization, phylogenetic relationships, gene structure, protein interaction network, cis-elements of promoters, tissue-specific expression and expression patterns under hormone treatment and abiotic stresses of these 40 KNOX genes were systematically studied. IbKNOX4, -5, and - 6 were highly expressed in the leaves of the high-yield varieties Longshu9 and Xushu18. IbKNOX3 and IbKNOX8 in Class I were upregulated in initial storage roots compared to fibrous roots. IbKNOXs in Class M were specifically expressed in the stem tip and hardly expressed in other tissues. Moreover, IbKNOX2 and - 6, and their homologous genes were induced by PEG/mannitol and NaCl treatments. The results showed that KNOXs were involved in regulating growth and development, hormone crosstalk and abiotic stress responses between sweet potato and its two diploid relatives. This study provides a comparison of these KNOX genes in sweet potato and its two diploid relatives and a theoretical basis for functional studies.


Assuntos
Diploide , Regulação da Expressão Gênica de Plantas , Ipomoea batatas , Família Multigênica , Filogenia , Proteínas de Plantas , Estresse Fisiológico , Ipomoea batatas/genética , Ipomoea batatas/crescimento & desenvolvimento , Ipomoea batatas/metabolismo , Estresse Fisiológico/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Genoma de Planta , Perfilação da Expressão Gênica , Regiões Promotoras Genéticas
15.
Nutrients ; 16(11)2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38892614

RESUMO

Aging and its related disorders are important issues nowadays and the first cause of this physio-pathological condition is the overproduction of ROS. Ascorbic acid is an antioxidant mediator and its anti-aging proprieties are well known. Our previous data demonstrated that Voghera sweet pepper (VP), a distinctive type of pepper cultivated in Italy, is particularly rich in ascorbic acid. Based on these data, the anti-aging effect mediated by extracts of the edible part of VP was evaluated on an in vitro model of both young and old Normal Human Diploid Fibroblasts (NHDF). Using phase contrast microscopy, we observed that VP may help cells in the maintenance of physiological morphology during aging. Cytofluorimetric analyses revealed that VP extracts led to an increase in DNA synthesis and percentage of living cells, linked to a consequent increase in mitotic events. This hypothesis is supported by the enhancement of PCNA expression levels observed in old, treated fibroblasts, corroborating the idea that this extract could recover a young phenotype in adult fibroblasts, confirmed by the study of p16 and p53 expression levels and TEM analyses. Based on these results, we may suppose that VP can lead to the partial recovery of "young-like" phenotypes in old fibroblasts.


Assuntos
Ácido Ascórbico , Capsicum , Proliferação de Células , Senescência Celular , Fibroblastos , Extratos Vegetais , Proteína Supressora de Tumor p53 , Humanos , Fibroblastos/efeitos dos fármacos , Fibroblastos/metabolismo , Capsicum/química , Senescência Celular/efeitos dos fármacos , Extratos Vegetais/farmacologia , Proliferação de Células/efeitos dos fármacos , Ácido Ascórbico/farmacologia , Proteína Supressora de Tumor p53/metabolismo , Antígeno Nuclear de Célula em Proliferação/metabolismo , Inibidor p16 de Quinase Dependente de Ciclina/metabolismo , Envelhecimento/fisiologia , Antioxidantes/farmacologia , Diploide , Células Cultivadas , Itália
16.
Molecules ; 29(11)2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38893545

RESUMO

Tetraploid oysters are artificially produced oysters that do not exist in nature. The successful breeding of 100% triploid oysters resolved the difficulties of traditional drug-induced triploids, such as the presence of drug residues and a low triploid induction rate. However, little is known concerning the biochemical composition and nutrient contents of such tetraploids. Therefore, we investigated compositional differences among diploid, triploid, and tetraploid Crassostrea gigas as well as between males and females of diploids and tetraploids. The findings indicated that glycogen, EPA, ∑PUFA, and omega-3 contents were significantly higher in triploid oysters than in diploids or tetraploids; tetraploid oysters had a significantly higher protein content, C14:0, essential amino acid, and flavor-presenting amino acid contents than diploids or triploids. For both diploid and tetraploids, females had significantly higher levels of glutamate, methionine, and phenylalanine than males but lower levels of glycine and alanine. In addition, female oysters had significantly more EPA, DHA, omega-3, and total fatty acids, a result that may be due to the fact that gonadal development in male oysters requires more energy to sustain growth, consumes greater amounts of nutrients, and accumulates more proteins. With these results, important information is provided on the production of C. gigas, as well as on the basis and backing for the genetic breeding of oysters.


Assuntos
Aminoácidos , Crassostrea , Diploide , Ácidos Graxos , Tetraploidia , Triploidia , Animais , Crassostrea/genética , Crassostrea/metabolismo , Aminoácidos/metabolismo , Ácidos Graxos/metabolismo , Ácidos Graxos/análise , Feminino , Masculino
17.
Metab Eng ; 84: 169-179, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38936763

RESUMO

7-Dehydrocholesterol (7-DHC) is widely present in various organisms and is an important precursor of vitamin D3. Despite significant improvements in the biosynthesis of 7-DHC, it remains insufficient to meet the industrial demands. In this study, we reported high-level production of 7-DHC in an industrial Saccharomyces cerevisiae leveraging subcellular organelles. Initially, the copy numbers of DHCR24 were increased in combination with sterol transcriptional factor engineering and rebalanced the redox power of the strain. Subsequently, the effects of compartmentalizing the post-squalene pathway in peroxisomes were validated by assembling various pathway modules in this organelle. Furthermore, several peroxisomes engineering was conducted to enhance the production of 7-DHC. Utilizing the peroxisome as a vessel for partial post-squalene pathways, the potential of yeast for 7-dehydrocholesterol production was demonstrated by achieving a 26-fold increase over the initial production level. 7-DHC titer reached 640.77 mg/L in shake flasks and 4.28 g/L in a 10 L bench-top fermentor, the highest titer ever reported. The present work lays solid foundation for large-scale and cost-effective production of 7-DHC for practical applications.


Assuntos
Desidrocolesteróis , Engenharia Metabólica , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Desidrocolesteróis/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Peroxissomos/metabolismo , Peroxissomos/genética , Diploide
18.
Plant Biol (Stuttg) ; 26(5): 735-748, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38924267

RESUMO

YABBY genes encode specific TFs of seed plants involved in development and formation of leaves, flowers, and fruit. In the present work, genome-wide and expression analyses of the YABBY gene family were performed in six species of the Fragaria genus: Fragaria × ananassa, F. daltoniana, F. nilgerrensis, F. pentaphylla, F. viridis, and F. vesca. The chromosomal location, synteny pattern, gene structure, and phylogenetic analyses were carried out. By combining RNA-seq data and RT-qPCR analysis we explored specific expression of YABBYs in F. × ananassa and F. vesca. We also analysed the promoter regions of FaYABBYs and performed MeJA application to F. × ananassa fruit to observe effects on gene expression. We identified and characterized 25 YABBY genes in F. × ananassa and six in each of the other five species, which belong to FIL/YAB3 (YABBY1), YAB2 (YABBY2), YAB5 (YABBY5), CRC, and INO clades previously described. Division of the YABBY1 clade into YABBY1.1 and YABBY1.2 subclades is reported. We observed differential expression according to tissue, where some FaYABBYs are expressed mainly in leaves and flowers and to a minor extent during fruit development of F. × ananassa. Specifically, the FaINO genes contain jasmonate-responsive cis-acting elements in their promoters which may be functional since FaINOs are upregulated in F. × ananassa fruit under MeJA treatment. This study suggests that YABBY TFs play an important role in the development- and environment-associated responses of the Fragaria genus.


Assuntos
Ciclopentanos , Diploide , Fragaria , Regulação da Expressão Gênica de Plantas , Oxilipinas , Filogenia , Proteínas de Plantas , Fatores de Transcrição , Fragaria/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Ciclopentanos/metabolismo , Ciclopentanos/farmacologia , Oxilipinas/farmacologia , Oxilipinas/metabolismo , Frutas/genética , Frutas/crescimento & desenvolvimento , Poliploidia , Acetatos/farmacologia , Regiões Promotoras Genéticas/genética , Sintenia , Família Multigênica
19.
Genome Biol ; 25(1): 163, 2024 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-38902799

RESUMO

BACKGROUND: Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome. RESULTS: While consistent results are observed for copy gain, loss, and loss of heterozygosity (LOH) calls across sequencing centers, CNV callers, and different technologies, variation of CNV calls are mostly affected by the determination of genome ploidy. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we establish a high confident CNV call set for the reference cancer cell line (HCC1395). CONCLUSIONS: NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.


Assuntos
Biologia Computacional , Variações do Número de Cópias de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Perda de Heterozigosidade , Neoplasias , Software , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias/genética , Biologia Computacional/métodos , Diploide , Genoma Humano , Linhagem Celular Tumoral , Reprodutibilidade dos Testes , Análise de Sequência de DNA/métodos
20.
Mar Environ Res ; 199: 106612, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38924833

RESUMO

Spores have crucial importance in the establishment and development of seaweed populations. When the spore release matches with the low tidal period, they experience an extreme variation in the environmental conditions including the temperature. In this study, we assess the photosynthetic responses and growth of haploid (tetraspores) and diploid (carpospores) spores of two Gigartinales species (Mazzaella laminarioides and Iridaea cordata) from sub-Antarctic populations when exposed to an increasing temperature. In the laboratory, freshly released spores were exposed to a temperature gradient (7 [control], 10, 15, and 20 °C) recreating the temperature increase experienced by these spores during typical spring tides. Germination and further growth of spores previously exposed to temperature treatments were assessed. Carpospores and tetraspores exhibited variation in their photosynthetic response (measured as effective quantum yield; ΦPSII) to temperature increase. In Mazzaella laminarioides, only carpospores exhibited a reduction in ΦPSII (by 7-24% at 15-20 °C), while both types of spores of Iridaea cordata were sensitive to temperature increase (12-24% of ΦPSII reduction at 10-20 °C). Spores previously exposed to temperature treatments and maintained at 7 °C and low PAR germinated and developed in germlings. In general, germlings originated from carpospores pre-treated at high temperatures showed higher growth rates. The different responses to temperature increase exhibited by haploid and diploid propagules of both species highlight their ecophysiological capacity to face high-temperature variation ensuring successful recruitment survival.


Assuntos
Diploide , Haploidia , Rodófitas , Esporos , Temperatura , Rodófitas/fisiologia , Rodófitas/genética , Esporos/fisiologia , Fotossíntese , Regiões Antárticas
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