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1.
Pestic Biochem Physiol ; 157: 80-87, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31153480

RESUMO

The European red mite Panonychus ulmi (Koch) is a major pest of apple trees worldwide and causes significant damage to apple orchards in Iran. Pyrethroid insecticides/acaricides, such as fenpropathrin and fenvalerate, are widely used to control P. ulmi, but their long-term use may lead to low efficacy. Earlier studies investigating pyrethroid resistance in closely related mites such as Tetranychus urticae revealed that pyrethroid resistance was associated with point mutations in the voltage-gated sodium channel gene (vgsc). The aim of this study was to investigate the biochemical and molecular mechanisms of fenpropathrin and fenvalerate resistance in Iranian populations of P. ulmi. Pyrethroid toxicity bioassays were carried out on different P. ulmi field populations. Marand (resistance ratio, RR = 149), Maraqeh (RR = 90) and Mianeh2 (RR = 71) populations exhibited high levels of resistance to fenpropathrin, compared to a susceptible field population (Shahin Dej). Resistance was also observed for fenvalerate with resistance ratio's ranging from 2- to 20-fold. Synergism experiments and enzyme activity assays predicted a minor role for classical detoxification enzymes. In contrast, two amino acid substitutions in the VGSC, L1024V and F1538I, that were previously shown to confer pyrethroid resistance, were detected in all three resistant P. ulmi populations and point towards target-site insensitivity as the most likely resistance mechanism. Furthermore, sequencing after cloning of vgsc fragments from single haploid males revealed the presence of multiple copies of vgsc in a highly resistant strain. The link between resistance mutations and vgsc copy number variation should be the subject of future study, as this might be used to develop molecular markers for monitoring pyrethroid resistance of P. ulmi in the field.


Assuntos
Mutação Puntual/genética , Piretrinas/farmacologia , Canais de Sódio Disparados por Voltagem/genética , Animais , Variações do Número de Cópias de DNA/genética , Duplicação Gênica/efeitos dos fármacos , Duplicação Gênica/genética , Resistência a Inseticidas/genética , Irã (Geográfico) , Ácaros , Canais de Sódio Disparados por Voltagem/metabolismo
2.
Nat Plants ; 5(5): 471-479, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31061537

RESUMO

Genome editing technologies are being widely adopted in plant breeding1. However, a looming challenge of engineering desirable genetic variation in diverse genotypes is poor predictability of phenotypic outcomes due to unforeseen interactions with pre-existing cryptic mutations2-4. In tomato, breeding with a classical MADS-box gene mutation that improves harvesting by eliminating fruit stem abscission frequently results in excessive inflorescence branching, flowering and reduced fertility due to interaction with a cryptic variant that causes partial mis-splicing in a homologous gene5-8. Here, we show that a recently evolved tandem duplication carrying the second-site variant achieves a threshold of functional transcripts to suppress branching, enabling breeders to neutralize negative epistasis on yield. By dissecting the dosage mechanisms by which this structural variant restored normal flowering and fertility, we devised strategies that use CRISPR-Cas9 genome editing to predictably improve harvesting. Our findings highlight the under-appreciated impact of epistasis in targeted trait breeding and underscore the need for a deeper characterization of cryptic variation to enable the full potential of genome editing in agriculture.


Assuntos
Domesticação , Epistasia Genética/genética , Duplicação Gênica/genética , Lycopersicon esculentum/genética , Proteína 9 Associada à CRISPR , Sistemas CRISPR-Cas , Flores/crescimento & desenvolvimento , Duplicação Gênica/fisiologia , Edição de Genes/métodos , Variação Genética/genética , Variação Genética/fisiologia , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/fisiologia , Melhoramento Vegetal , Plantas Geneticamente Modificadas , Locos de Características Quantitativas/genética , Reprodução/genética , Reprodução/fisiologia
3.
Nat Commun ; 10(1): 2037, 2019 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-31048690

RESUMO

Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer (GC) tumorigenesis. Here, we analysis structural variations (SVs) and mutational signatures via whole-genome sequencing of 168 GCs. Our data demonstrates diverse models of complex SVs operative in GC, which lead to high-level amplification of oncogenes. We find varying proportion of tandem-duplications (TDs) among individuals and identify 24 TD hotspots involving well-established cancer genes such as CCND1, ERBB2 and MYC. Specifically, we nominate a novel hotspot involving the super-enhancer of ZFP36L2 presents in approximately 10% GCs from different cohorts, the oncogenic role of which is further confirmed by experimental data. In addition, our data reveal a mutational signature, specifically occurring in noncoding region, significantly enriched in tumors with cadherin 1 mutations, and associated with poor prognoses. Collectively, our data suggest that TDs might serve as an important mechanism for cancer gene activation and provide a novel signature for stratification.


Assuntos
Oncogenes/genética , Neoplasias Gástricas/genética , Fatores de Transcrição/genética , Transcriptoma/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Antígenos CD/genética , Caderinas/genética , Carcinogênese/genética , Linhagem Celular Tumoral , Elementos Facilitadores Genéticos/genética , Éxons/genética , Feminino , Duplicação Gênica/genética , Variação Estrutural do Genoma , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Estômago/patologia , Neoplasias Gástricas/mortalidade , Neoplasias Gástricas/patologia , Análise de Sobrevida , Sequenciamento Completo do Genoma
4.
Gene ; 698: 129-140, 2019 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-30849535

RESUMO

Rainbow trout have, as salmonid fish species, undergone sequential genome duplication events in their evolutionary history. In addition to a teleost-specific whole genome duplication approximately 320-350 million years ago, rainbow trout and salmonids in general underwent an additional salmonid lineage-specific genome duplication event approximately 80 million years ago. Through the recent sequencing of salmonid genome sequences, including the rainbow trout, the identification and study of duplicated genes has become available. A particular focus of interest has been the evolution and regulation of rainbow trout gluconeogenic genes, as recent molecular and gene expression evidence points to a possible contribution of previously uncharacterized gluconeogenic gene paralogues to the rainbow trout long-studied glucose intolerant phenotype. Since the publication of the initial rainbow trout genome draft, resequencing and annotation have further improved genome coverage. Taking advantage of these recent improvements, we here identify a salmonid-specific genome duplication of ancestral mitochondrial phosphoenolpyruvate carboxykinase 2 isoenzyme, we termed pck2a and pck2b. Cytosolic phosphoenolpyruvate carboxykinase (Pck1) and, more recently mitochondrial Pck2, are considered to be the rate-limiting enzymes in de novo gluconeogenesis. Following in silico confirmation of salmonid pck2a and pck2b evolutionary history, we simultaneously profiled cytosolic pck1 and mitochondrial pck2a and pck2b expression in rainbow trout liver under several experimental conditions known to regulate hepatic gluconeogenesis. Cytosolic pck1 abundance was increased by nutritional (diets with a high protein to carbohydrate ratio compared to diets with a low carbohydrate to protein ratio) and glucoregulatory endocrine factors (glucagon and cortisol), revealing that the well-described transcriptional regulation of pck1 in mammals is present in rainbow trout. Conversely, and in contrast to mammals, we here describe endocrine regulation of pck2a (decrease in abundance in response to glucagon infusion), and nutritional, social-status-dependent and hypoxia-dependent regulation of pck2b. Specifically, pck2b transcript abundance increased in trout fed a diet with a low protein to carbohydrate ratio compared to a diet with a high protein to carbohydrate ratio, in dominant fish compared to subordinate fish as well as hypoxia. This specific and differential expression of rainbow trout pck2 ohnologues is indicative of functional diversification, and possible functional consequences are discussed in light of the recently highlighted gluconeogenic roles of mitochondrial pck2 in mammalian models.


Assuntos
Duplicação Gênica/genética , Oncorhynchus mykiss/genética , Fosfoenolpiruvato Carboxiquinase (ATP)/genética , Animais , Mapeamento Cromossômico/métodos , Evolução Molecular , Regulação da Expressão Gênica/genética , Genoma/genética , Gluconeogênese/genética , Glucose/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/genética , Oncorhynchus mykiss/metabolismo , Fosfoenolpiruvato Carboxiquinase (ATP)/metabolismo , Filogenia , Análise de Sequência de Proteína/métodos
5.
Gene ; 698: 61-71, 2019 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-30825597

RESUMO

Phosphoenolpyruvate carboxylase (PEPC) family genes play important roles in regulating plant growth and abiotic stress response. Based on the sequenced Gossypium genomes, we performed comprehensive analysis of PEPC homolog genes in cotton, which six, six, eleven and ten PEPC genes were identified in Gossypium arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2), respectively. These genes were divided into six subgroups: PEPC-i, PEPC-ii, PEPC-iii, PEPC-iv, PEPC-v and PEPC-vi; PEPC genes in each subgroup displayed conserved gene structure and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Of which, genes in PEPC-iv subgroup played crucial role for substrate distribution in cottonseed. Cis-elements, putative miRNAs and expression analyses showed that GhPEPC homologs might respond to abiotic stresses, expression levels of GhPEPC1 and GhPEPC2/GhPEPC2D genes were larger induced than other GhPEPC genes under cold, heat, salt, and drought stresses, indicating the crucial roles in abiotic stresses response. Present study serves new information to decipher the evolution and function of PEPC genes in Gossypium.


Assuntos
Gossypium/genética , Fosfoenolpiruvato Carboxilase/genética , Estresse Fisiológico/genética , Mapeamento Cromossômico/métodos , Evolução Molecular , Duplicação Gênica/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla/métodos , Fosfoenolpiruvato Carboxilase/metabolismo , Filogenia , Proteínas de Plantas/genética , Estresse Fisiológico/fisiologia
6.
Mol Biol Rep ; 46(2): 1941-1954, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30710231

RESUMO

Heat shock proteins 70 (Hsp70) constitute a highly conserved protein family of cellular chaperones widely distributed in plants, where they play a fundamental role in response to biotic and abiotic stress. Until now, genome-wide analyses of the Hsp70 gene family have been conducted for some species. However, reports about Hsp70 genes in Nicotiana tabacum are scarce. In this study, we systematically conducted genome-wide identification and expression analysis of the Hsp70 gene family in tobacco, including gene structure, classification, evolutionary relationships, promoters, and transcript levels in response to abiotic stress treatments. In all, 61 Hsp70 members were identified and classified into six groups that were mapped onto 18 chromosomes, where most were distributed on both ends of the chromosome. The conserved structures and motifs of NtHsp70 proteins in the same subfamily were highly consistent. At least 15 pairs of NtHsp70 genes underwent gene duplication by segment and tandem duplications. Most NtHsp70 proteins contained N-terminal hexokinase conserved motifs. Phylogenetic analysis showed that most species expanded according to their own species-specific approach during the evolution of Hsp70s. Tissue-specific expression analysis indicated that all NtHsp70 genes were involved in at least one or more abiotic stress responses, highlighting the wide participation of NtHsp70 genes in environmental adaptation. This is the first genome-wide analysis of Hsp70 in N. tabacum. These results indicate that each NtHsp70 member fulfilled distinct functions in response to various abiotic stresses.


Assuntos
Proteínas de Choque Térmico HSP70/genética , Proteínas de Choque Térmico HSP70/metabolismo , Tabaco/genética , Evolução Molecular , Duplicação Gênica/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Estudo de Associação Genômica Ampla , Proteínas de Choque Térmico HSP70/classificação , Chaperonas Moleculares/genética , Família Multigênica , Filogenia , Proteínas de Plantas/genética , Estresse Fisiológico/genética , Tabaco/metabolismo
7.
Nucleic Acids Res ; 47(7): 3503-3520, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-30715513

RESUMO

The primary function of the UBE2T ubiquitin conjugase is in the monoubiquitination of the FANCI-FANCD2 heterodimer, a central step in the Fanconi anemia (FA) pathway. Genetic inactivation of UBE2T is responsible for the phenotypes of FANCT patients; however, a FANCT patient carrying a maternal duplication and a paternal deletion in the UBE2T loci displayed normal peripheral blood counts and UBE2T protein levels in B-lymphoblast cell lines. To test whether reversion by recombination between UBE2T AluYa5 elements could have occurred in the patient's hematopoietic stem cells despite the defects in homologous recombination (HR) in FA cells, we constructed HeLa cell lines containing the UBE2T AluYa5 elements and neighboring intervening sequences flanked by fluorescent reporter genes. Introduction of a DNA double strand break in the model UBE2T locus in vivo promoted single strand annealing (SSA) between proximal Alu elements and deletion of the intervening color marker gene, recapitulating the reversion of the UBE2T duplication in the FA patient. To test whether UBE2T null cells retain HR activity, the UBE2T genes were knocked out in HeLa cells and U2OS cells. CRISPR/Cas9-mediated genetic knockout of UBE2T only partially reduced HR, demonstrating that UBE2T-independent pathways can compensate for the recombination defect in UBE2T/FANCT null cells.


Assuntos
Elementos Alu/genética , Anemia de Fanconi/genética , Recombinação Homóloga/genética , Enzimas de Conjugação de Ubiquitina/genética , Sistemas CRISPR-Cas/genética , Quebras de DNA de Cadeia Dupla , Dano ao DNA/genética , Anemia de Fanconi/patologia , Proteína do Grupo de Complementação D2 da Anemia de Fanconi/genética , Proteínas de Grupos de Complementação da Anemia de Fanconi/genética , Deleção de Genes , Duplicação Gênica/genética , Células HeLa , Células-Tronco Hematopoéticas/metabolismo , Humanos , Herança Materna/genética , Herança Paterna/genética
8.
Psychiatr Genet ; 29(3): 86-90, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30724859

RESUMO

About one child in 68 is affected by the autism spectrum disorder (ASD), one of the most common neurodevelopmental disorders linked to intellectual disability, especially in males, intellectual disability being diagnosable in about 60-70% of autistic individuals. The biological bases of ASD are not yet fully known, but they are generally considered multifactorial, although many genes and genomic loci have been proposed to be possibly associated with this condition. In this report, we describe the case of a 14-year-old female Italian proband affected by ASD, carrying a novel ~ 270 kb interstitial microduplication, localized at the distal portion of the 4q13.1 region. The rearrangement was inherited from a mild symptomatic father and included a large part of the single EPHA5 gene, a receptor tyrosine kinase involved in the neural development, already indicated to be linked to ASD by previous Genome Wide Association Studies. This imbalance represents, to the best of our knowledge, the smallest duplication identified to date that only impacts the EPHA5 gene. We hypothesize that the duplication of this gene may alter EPHA5 expression and that this may impact the autistic phenotype of the patient.


Assuntos
Transtorno do Espectro Autista/genética , Receptor EphA5/genética , Adolescente , Transtorno Autístico/genética , Hibridização Genômica Comparativa , Feminino , Duplicação Gênica/genética , Estudo de Associação Genômica Ampla , Genômica , Humanos , Deficiência Intelectual/genética , Itália , Fenótipo , Receptor EphA5/fisiologia
9.
J Med Microbiol ; 68(2): 263-278, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30628877

RESUMO

PURPOSE: Burkholderia pseudomallei, the tier 1 agent of melioidosis, is a saprophytic microbe that causes endemic infections in tropical regions such as South-East Asia and Northern Australia. It is globally distributed, challenging to diagnose and treat, infectious by several routes including inhalation, and has potential for adversarial use. B. pseudomallei strain MSHR5848 produces two colony variants, smooth (S) and rough (R), which exhibit a divergent range of morphological, biochemical and metabolic phenotypes, and differ in macrophage and animal infectivity. We aimed to characterize two major phenotypic differences, analyse gene expression and study the regulatory basis of the variation. METHODOLOGY: Phenotypic expression was characterized by DNA and RNA sequencing, microscopy, and differential bacteriology. Regulatory genes were identified by cloning and bioinformatics.Results/Key findings. Whereas S produced larger quantities of extracellular DNA, R was upregulated in the production of a unique chromosome 1-encoded Siphoviridae-like bacteriophage, φMSHR5848. Exploratory transcriptional analyses revealed significant differences in variant expression of genes encoding siderophores, pili assembly, type VI secretion system cluster 4 (T6SS-4) proteins, several exopolysaccharides and secondary metabolites. A single 3 base duplication in S was the only difference that separated the variants genetically. It occurred upstream of a cluster of bacteriophage-associated genes on chromosome 2 that were upregulated in S. The first two genes were involved in regulating expression of the multiple phenotypes distinguishing S and R. CONCLUSION: Bacteriophage-associated proteins have a major role in the phenotypic expression of MSHR5848. The goals are to determine the regulatory basis of this phenotypic variation and its role in pathogenesis and environmental persistence of B. pseudomallei.


Assuntos
Bacteriófagos/genética , Burkholderia pseudomallei/genética , Melioidose/microbiologia , Bacteriófagos/isolamento & purificação , Bacteriófagos/ultraestrutura , Burkholderia pseudomallei/classificação , Burkholderia pseudomallei/virologia , Clonagem Molecular , Biologia Computacional , DNA Bacteriano/química , DNA Bacteriano/isolamento & purificação , DNA Viral/análise , DNA Viral/química , DNA Viral/isolamento & purificação , Duplicação Gênica/genética , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Genes Reguladores , Humanos , Microscopia Eletrônica , Família Multigênica , Myoviridae/genética , Myoviridae/isolamento & purificação , Myoviridae/ultraestrutura , Fenótipo , RNA Bacteriano/análise , RNA Bacteriano/química , RNA Bacteriano/isolamento & purificação , Análise de Sequência de DNA , Análise de Sequência de RNA
11.
Methods Mol Biol ; 1851: 49-62, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30298391

RESUMO

Gene duplication is an important process in the evolution of gene content in eukaryotic genomes. Understanding when gene duplicates contribute new molecular functions to genomes through molecular adaptation is one important goal in comparative genomics. In large gene families, however, characterizing adaptation and neofunctionalization across species is challenging, as models have traditionally quantified the timing of duplications without considering underlying gene trees. This protocol combines multiple approaches to detect adaptation in protein duplicates at a phylogenetic scale. We include a description of models for gene tree-species tree reconciliation that enable different types of inference, as well as a practical guide to their use. Although simulation-based approaches successfully detect shifts in the rate of duplication/retention, the conflation between the duplication and retention processes, the distinct trajectories of duplicates under non-, sub-, and neofunctionalization, as well as dosage effects offer hitherto unexplored analytical avenues. We introduce mathematical descriptions of these probabilities and offer a road map to computational implementation whose starting point is parsimony reconciliation. Sequence evolution information based on the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) can be combined with duplicate survival probabilities to better predict the emergence of new molecular functions in retained duplicates. Together, these methods enable characterization of potentially adaptive candidate duplicates whose neofunctionalization may contribute to phenotypic divergence across species.


Assuntos
Evolução Molecular , Proteínas de Membrana/genética , Duplicação Gênica/genética , Genes Duplicados/genética , Genômica , Proteínas de Membrana/classificação , Filogenia
12.
Gene ; 688: 132-139, 2019 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-30529096

RESUMO

To investigate whether the members of the mammalian Achaete-Scute Complex homologue (ASH) gene family have evolved functional differences, we used the patterning of bristles as a phenotypic marker. Drosophila uses a single genetic locus - the Achaete-Scute Complex - to demarcate the regions of the body where bristles can form. We found 4-5 Achaete-Scute Complex homologue genes (ASH) in the mammalian genome, which are homologous with scute in Drosophila. Although ASH2 and ASH3 have gained new functions during evolution, the function of ASH4 and its evolutionary changes are still unclear. In this study, we overexpressed mouse and human ASH1 and ASH4 in the Drosophila notum respectively. The results show that both the protein sequence and cis-regulatory elements of mammalian ASH1 have conserved an ancient proneural function during evolution. However, mouse ASH4 has lost proneural function partly due to truncation of a C-terminal amino acid domain. Interestingly, instead of a similar loss of proneural function, we found human ASH4 can actually inhibit Drosophila bristle development, implying that human ASH4 may be a potential factor relating to skin development in human being. Our results demonstrate gene duplication of the ASH family may have led to a novel function during evolution.


Assuntos
Drosophila/genética , Mamíferos/genética , Neurogênese/genética , Sequências Reguladoras de Ácido Nucleico/genética , Fatores de Transcrição/genética , Animais , Sequência de Bases , Evolução Biológica , Padronização Corporal/genética , Sequência Conservada , Duplicação Gênica/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Humanos , Camundongos
13.
Nat Commun ; 9(1): 5319, 2018 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-30552336

RESUMO

Disorders of sex development (DSDs) are conditions affecting development of the gonads or genitalia. Variants in two key genes, SRY and its target SOX9, are an established cause of 46,XY DSD, but the genetic basis of many DSDs remains unknown. SRY-mediated SOX9 upregulation in the early gonad is crucial for testis development, yet the regulatory elements underlying this have not been identified in humans. Here, we identified four DSD patients with overlapping duplications or deletions upstream of SOX9. Bioinformatic analysis identified three putative enhancers for SOX9 that responded to different combinations of testis-specific regulators. All three enhancers showed synergistic activity and together drive SOX9 in the testis. This is the first study to identify SOX9 enhancers that, when duplicated or deleted, result in 46,XX or 46,XY sex reversal, respectively. These enhancers provide a hitherto missing link by which SRY activates SOX9 in humans, and establish SOX9 enhancer mutations as a significant cause of DSD.


Assuntos
Transtornos do Desenvolvimento Sexual/genética , Duplicação Gênica/genética , Fatores de Transcrição SOX9/genética , Fatores de Transcrição SOX9/metabolismo , Deleção de Sequência/genética , Proteína da Região Y Determinante do Sexo/genética , Transtornos 46, XX do Desenvolvimento Sexual/genética , Animais , Linhagem Celular , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Transtorno 46,XY do Desenvolvimento Sexual/genética , Feminino , Técnicas de Inativação de Genes , Genitália/metabolismo , Gônadas/metabolismo , Humanos , Masculino , Camundongos , Mutação , Fatores de Processamento de RNA/metabolismo , Sequências Reguladoras de Ácido Nucleico/genética , Fatores de Transcrição SOX/genética , Diferenciação Sexual , Testículo/crescimento & desenvolvimento , Testículo/metabolismo
14.
BMC Plant Biol ; 18(1): 368, 2018 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-30577806

RESUMO

BACKGROUND: Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system. RESULTS: The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae. CONCLUSIONS: We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.


Assuntos
Cleome/genética , Flores/crescimento & desenvolvimento , Proteínas de Domínio MADS/genética , Proteínas de Plantas/genética , Arabidopsis/genética , Brassicaceae/genética , Cleome/crescimento & desenvolvimento , Flores/genética , Duplicação Gênica/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Variação Genética/genética , Proteínas de Domínio MADS/fisiologia , Filogenia , Proteínas de Plantas/fisiologia , Alinhamento de Sequência
15.
PLoS One ; 13(12): e0209381, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30571741

RESUMO

The following research was conducted to elucidate the evolution and expression of salmonid selenoprotein P (SelP), a selenoprotein that is unique in having multiple selenocysteine (Sec) residues, following supranutritional selenium supplementation and infection in rainbow trout. We show that in salmonids SelP is present as four paralogues and that the diversification of SelP genes during vertebrate evolution relates to whole genome duplication events. With 17 and 16 selenocysteine residues for rainbow trout (Oncorhynchus mykiss)/Atlantic salmon (Salmo salar) SelPa1 and SelPa2 proteins respectively and 1 or 2 (trout or salmon) and 4 or 3 (trout or salmon) selenocysteine residues for salmonid SelPb1 and SelPb2 proteins respectively, this is the highest number of (predicted) multiple selenocysteine containing SelP proteins reported for any vertebrate species to date. To investigate the effects of selenium form on SelP expression we added different concentrations (1 nM- 10 µM) of organic or inorganic selenium to a trout cell line (RTG-2 cells) and analysed changes in mRNA abundance. We next studied the impact of supplementation on the potential modulation of these transcripts by PAMPs and proinflammatory cytokines in RTG-2 and RTS-11 cells. These experiments revealed that selenium type influenced the responses, and that SelP gene subfunctionalisation was apparent. To get an insight into the expression patterns in vivo we conducted a feeding trial with 2 diets differing in selenium content and 5 weeks later challenged the trout with a bacterial pathogen (Aeromonas salmonicida). Four tissues were analysed for SelP paralogue expression. The results show a significant induction of SelPa1 in gills and intestine following infection in selenium supplemented fish and for SelPa2 in gills. SelPb1 was significantly reduced in head kidney of both diet groups following infection, whilst SelPb2 was significantly upregulated in skin of both diet groups post infection. Overall these findings reveal differential expression profiles for the SelPa/SelPb paralogues in trout, influenced by selenium supply, cell type/tissue and stimulant. The increase of multiple Sec containing SelP proteins in salmonids could indicate an enhanced requirement for selenium in this lineage.


Assuntos
Antioxidantes/administração & dosagem , Oncorhynchus mykiss/genética , Salmo salar/genética , Selênio/administração & dosagem , Selenoproteína P/genética , Aeromonas salmonicida/imunologia , Aeromonas salmonicida/patogenicidade , Sequência de Aminoácidos/genética , Ração Animal , Animais , Aquicultura/métodos , Linhagem Celular , Furunculose/imunologia , Furunculose/microbiologia , Furunculose/prevenção & controle , Duplicação Gênica/genética , Duplicação Gênica/imunologia , Infecções por Bactérias Gram-Negativas/imunologia , Infecções por Bactérias Gram-Negativas/microbiologia , Infecções por Bactérias Gram-Negativas/prevenção & controle , Infecções por Bactérias Gram-Negativas/veterinária , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Oncorhynchus mykiss/metabolismo , Oncorhynchus mykiss/microbiologia , RNA Mensageiro/metabolismo , Salmo salar/metabolismo , Salmo salar/microbiologia , Selenocisteína/genética , Selenoproteína P/imunologia , Selenoproteína P/metabolismo , Regulação para Cima/efeitos dos fármacos
16.
Plant Cell Physiol ; 59(11): 2169-2187, 2018 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-30169685

RESUMO

Small regulatory RNAs guide gene silencing at the DNA or RNA level through repression of complementary sequences. The two main forms of small RNAs are microRNA (miRNA) and small interfering RNA (siRNAs), which are generated from the processing of different forms of double-stranded RNA (dsRNA) precursors. These two forms of small regulatory RNAs function in distinct but overlapping gene silencing pathways in plants. Gene silencing pathways in eukaryotes evolved from an ancient prokaryotic mechanism involved in genome defense against invasive genetic elements, but has since diversified to also play a crucial role in regulation of endogenous gene expression. Here, we review the biogenesis of the different forms of small RNAs in plants, including miRNAs, phased, secondary siRNAs (phasiRNAs) and heterochromatic siRNAs (hetsiRNAs), with a focus on their functions in genome defense, transcriptional and post-transcriptional gene silencing, RNA-directed DNA methylation, trans-chromosomal methylation and paramutation. We also discuss the important role that gene duplication has played in the functional diversification of gene silencing pathways in plants, and we highlight recently discovered components of gene silencing pathways in plants.


Assuntos
Evolução Molecular , Magnoliopsida/genética , Pequeno RNA não Traduzido/metabolismo , Duplicação Gênica/genética , Inativação Gênica , Variação Genética/genética , Magnoliopsida/metabolismo , Pequeno RNA não Traduzido/genética
17.
Planta ; 248(5): 1187-1199, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30094488

RESUMO

MAIN CONCLUSION: Sugar transport, including the symplasmic pathway in plasmodesmata and apoplasmic pathway mediated by sugar transporters, accelerated sugar accumulation in cultivated jujube, while sugar metabolism-related genes played weak roles in jujube domestication. The fruit of Chinese jujube (Ziziphus jujuba Mill.) is high in sugar concentration. By contrast, wild type-sour jujube (Z. jujuba Mill. var. spinosa Hu) contains markedly less sugar. It is unknown whether sugar transport or sugar metabolism drove sugar accumulation during jujube domestication. Using a combination of ultrastructural observations, phylogenetic analysis, testing for soluble sugars, and transcriptional analysis, the sugar accumulation mechanism was studied in the developmental stages of cultivated jujube and sour jujube. Our results indicate that the symplasmic transport pathway in plasmodesmata is present in cultivated jujube, but not in sour jujube. Sugar transporter genes have higher frequencies of duplication than sugar metabolism-related genes. Gene expression patterns indicate that sugar transporter genes, especially ZjSUT2, ZjSWEET1, ZjSWEET7, ZjSWEET11, ZjSTP3, and ZjSTP13a, rather than sugar metabolism-related genes showed higher expression levels in cultivated jujube versus sour jujube during fruit sugar accumulation. These findings suggest that sugar transport, including apoplasmic and symplasmic transport, rather than sugar biosynthesis, is associated with the difference in sugar accumulation between jujube and sour jujube, and that it may drive jujube domestication. This study provides valuable genetic information for jujube improvement, and offers new insights into fruit tree domestication related to sugar accumulation.


Assuntos
Açúcares/metabolismo , Ziziphus/metabolismo , Metabolismo dos Carboidratos/genética , Cromossomos de Plantas/genética , Domesticação , Frutas/química , Frutas/crescimento & desenvolvimento , Duplicação Gênica/genética , Redes e Vias Metabólicas/genética , Microscopia Eletrônica de Transmissão , Floema/ultraestrutura , Filogenia , Plasmodesmos/metabolismo , Plasmodesmos/ultraestrutura , Açúcares/análise , Ziziphus/genética , Ziziphus/ultraestrutura
18.
Int J Mol Sci ; 19(8)2018 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-30065178

RESUMO

The insect GABA receptor, RDL (resistance to dieldrin), is a cys-loop ligand-gated ion channel (cysLGIC) that plays a central role in neuronal signaling, and is the target of several classes of insecticides. Many insects studied to date possess one Rdl gene; however, there is evidence of two Rdls in aphids. To characterise further this insecticide target from pests that cause millions of dollars' worth of crop damage each year, we identified the complete cysLGIC gene superfamily of the pea aphid, Acyrthosiphon pisum, using BLAST analysis. This confirmed the presence of two Rdl-like genes (RDL1 and RDL2) that likely arose from a recent gene duplication. When expressed individually in Xenopus laevis oocytes, both subunits formed functional ion channels gated by GABA. Alternative splicing of RDL1 influenced the potency of GABA, and the potency of fipronil was different on the RDL1bd splice variant and RDL2. Imidacloprid and clothianidin showed no antagonistic activity on RDL1, whilst 100 µM thiacloprid reduced the GABA responses of RDL1 and RDL2 to 55% and 62%, respectively. It was concluded that gene duplication of Rdl may have conferred increased tolerance to natural insecticides, and played a role in the evolution of insect cysLGICs.


Assuntos
Processamento Alternativo/efeitos dos fármacos , Afídeos/genética , Processamento Alternativo/genética , Animais , Afídeos/efeitos dos fármacos , Duplicação Gênica/efeitos dos fármacos , Duplicação Gênica/genética , Resistência a Inseticidas/genética , Inseticidas/farmacologia , Neonicotinoides/farmacologia , Pirazóis/farmacologia , Tiazinas/farmacologia
19.
Gene ; 677: 232-244, 2018 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-30025926

RESUMO

Calmodulin (CaM) and calmodulin-like (CML) proteins are two kinds of calcium (Ca2+)-sensing proteins that are involved in Ca2+-signaling processes. B. rapa and B. oleracea are two of three diploid Brassica species that have undergone recent additional Brassiceae-lineage-specific whole-genome triplication events. To elucidate the expansion, evolution, expression pattern and interaction network of these Ca2+ sensors in B. rapa and B. oleracea, we conducted a comparative syntenic study on a genome-wide level using Arabidopsis thaliana. In total, 80 and 79 CaM/CML genes were identified in B. rapa and B. oleracea, respectively. The CaM/CML genes have expanded throughout the whole genomes of B. rapa and B. oleracea by whole-genome and tandem duplication events. The CaMs/CMLs of B. rapa and B. oleracea can be classified into nine subgroups based on their A. thaliana orthologs. Expression data from various tissues revealed that a large portion of CaM/CML genes exhibited patterns of differential and tissue-specific expression. The expression levels among duplicated paralogs in different subgenomes demonstrated the expression divergence of these genes in B. rapa and B. oleracea. The differential expressions of duplicated CaM and CML genes in B. rapa indicated that their functional differentiation occurred after polyploidization. The construction of interaction network and GO enrichment analysis of genes in this network revealed Br/BoCaMs/CMLs involving biological processes. This work will promote a better understanding of Ca2+ sensors and Ca2+-signaling pathways in B. rapa and B. oleracea.


Assuntos
Brassica rapa/genética , Brassica/genética , Calmodulina/genética , Genoma de Planta/genética , Arabidopsis/genética , Cálcio/metabolismo , Mapeamento Cromossômico/métodos , Evolução Molecular , Duplicação Gênica/genética , Estudo de Associação Genômica Ampla/métodos , Genômica/métodos , Filogenia , Transdução de Sinais/genética
20.
Genes Genomics ; 40(5): 465-473, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29892954

RESUMO

Gender Dysphoria is characterized by a marked incongruence between the cerebral sex and biological sex. To investigate the possible influence of karyotype on the etiology of Gender Dysphoria we carried out the cytogenetic analysis of karyotypes in 444 male-to-females (MtFs) and 273 female-to-males (FtMs) that attended the Gender Identity Units of Barcelona and Málaga (Spain) between 2000 and 2016. The karyotypes from 23 subjects (18 MtFs and 5 FtMs) were also analysed by Affymetrix CytoScan™ high-density (HD) arrays. Our data showed a higher incidence of cytogenetic alterations in Gender Dysphoria (2.65%) than in the general population (0.53%) (p < 0.0001). When G-banding was performed, 11 MtFs (2.48%) and 8 FtMs (2.93%) showed a cytogenetic alteration. Specifically, Klinefelter syndrome frequency was significantly higher (1.13%) (p < 0.0001), however Turner syndrome was not represented in our sample (p < 0.61). At molecular level, HD microarray analysis revealed a 17q21.31 microduplication which encompasses the gene KANSL1 (MIM612452) in 5 out of 18 MtFs and 2 out of 5 FtMs that corresponds to a copy-number variation region in chromosome 17q21.31. In conclusion, we confirm a significantly high frequency of aneuploidy, specifically Klinefelter syndrome and we identified in 7 out of 23 GD individuals the same microduplication of 572 Kb which encompasses the KANSL1 gene.


Assuntos
Disforia de Gênero/etiologia , Disforia de Gênero/genética , Cariotipagem/métodos , Adulto , Bandeamento Cromossômico/métodos , Cromossomos Humanos Par 17/genética , Feminino , Identidade de Gênero , Duplicação Gênica/genética , Humanos , Cariótipo , Síndrome de Klinefelter , Masculino , Pessoa de Meia-Idade , Proteínas Nucleares/genética , Transexualismo/genética , Síndrome de Turner
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