RESUMO
Proteostasis collapse, the diminished ability to maintain protein homeostasis, has been established as a hallmark of nematode aging. However, whether proteostasis collapse occurs in humans has remained unclear. Here, we demonstrate that proteostasis decline is intrinsic to human senescence. Using transcriptome-wide characterization of gene expression, splicing, and translation, we found a significant deterioration in the transcriptional activation of the heat shock response in stressed senescent cells. Furthermore, phosphorylated HSF1 nuclear localization and distribution were impaired in senescence. Interestingly, alternative splicing regulation was also dampened. Surprisingly, we found a decoupling between different unfolded protein response (UPR) branches in stressed senescent cells. While young cells initiated UPR-related translational and transcriptional regulatory responses, senescent cells showed enhanced translational regulation and endoplasmic reticulum (ER) stress sensing; however, they were unable to trigger UPR-related transcriptional responses. This was accompanied by diminished ATF6 nuclear localization in stressed senescent cells. Finally, we found that proteasome function was impaired following heat stress in senescent cells, and did not recover upon return to normal temperature. Together, our data unraveled a deterioration in the ability to mount dynamic stress transcriptional programs upon human senescence with broad implications on proteostasis control and connected proteostasis decline to human aging.
Assuntos
Envelhecimento/fisiologia , Senescência Celular/fisiologia , Proteostase/genética , Ativação Transcricional/fisiologia , Fator 6 Ativador da Transcrição/metabolismo , Linhagem Celular , Núcleo Celular/metabolismo , Estresse do Retículo Endoplasmático/genética , Resposta ao Choque Térmico/genética , Humanos , Complexo de Endopeptidases do Proteassoma/metabolismo , Biossíntese de Proteínas , RNA-Seq , Resposta a Proteínas não Dobradas/genéticaRESUMO
Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive. Here we present a genome-wide mapping of transcriptional readthrough, using nuclear RNA-Seq, comparing heat shock, osmotic stress, and oxidative stress in NIH 3T3 mouse fibroblast cells. We observe massive induction of transcriptional readthrough, both in levels and length, under all stress conditions, with significant, yet not complete, overlap of readthrough-induced loci between different conditions. Importantly, our analyses suggest that stress-induced transcriptional readthrough is not a random failure process, but is rather differentially induced across different conditions. We explore potential regulators and find a role for HSF1 in the induction of a subset of heat shock-induced readthrough transcripts. Analysis of public datasets detected increases in polymerase II occupancy in DoG regions after heat shock, supporting our findings. Interestingly, DoGs tend to be produced in the vicinity of neighboring genes, leading to a marked increase in their antisense-generating potential. Finally, we examine genomic features of readthrough transcription and observe a unique chromatin signature typical of DoG-producing regions, suggesting that readthrough transcription is associated with the maintenance of an open chromatin state.
Assuntos
Regulação da Expressão Gênica , Genoma , Genômica/métodos , Resposta ao Choque Térmico , Pressão Osmótica , Estresse Oxidativo , Transcrição Gênica , Animais , Perfilação da Expressão Gênica , Camundongos , Células NIH 3T3RESUMO
Naturally occurring stress-induced transcriptional readthrough is a recently discovered phenomenon, in which stress conditions lead to dramatic induction of long transcripts as a result of transcription termination failure. In 2015, we reported the induction of such downstream of gene (DoG) containing transcripts upon osmotic stress in human cells, while others observed similar transcripts in virus-infected and cancer cells. Using the rigorous methodology Cap-Seq, we demonstrated that DoGs result from transcriptional readthrough, not de novo initiation. More recently, we presented a genome-wide comparison of NIH3T3 mouse cells subjected to osmotic, heat, and oxidative stress and concluded that massive induction of transcriptional readthrough is a hallmark of the mammalian stress response. In their recent letter, Huang and Liu in contrast claim that DoG transcripts result from novel transcription initiation near the ends of genes. Their conclusions rest on analyses of a publicly available transcription start site (TSS-Seq) dataset from unstressed NIH3T3 cells. Here, we present evidence that this dataset identifies not only true transcription start sites, TSSs, but also 5'-ends of numerous snoRNAs, which are generally processed from introns in mammalian cells. We show that failure to recognize these erroneous assignments in the TSS-Seq dataset, as well as ignoring published Cap-Seq data on TSS mapping during osmotic stress, have led to misinterpretation by Huang and Liu. We conclude that, contrary to the claims made by Huang and Liu, TSS-Seq reads near gene ends cannot explain the existence of DoGs, nor their stress-mediated induction. Rather it is, as we originally demonstrated, transcriptional readthrough that leads to the formation of DoGs.
Assuntos
RNA Nucleolar Pequeno/genética , Estresse Fisiológico/genética , Sítio de Iniciação de Transcrição , Transcriptoma/genética , Animais , Regulação da Expressão Gênica/genética , Sequenciamento de Nucleotídeos em Larga Escala , Camundongos , Células NIH 3T3 , Regiões Promotoras GenéticasRESUMO
BACKGROUND: Recent studies have described a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying naturally occurring transcriptional readthrough, as well as its regulatory consequences, still remain elusive. Furthermore, the readthrough response to stress has thus far not been investigated outside of mammalian species, and the occurrence of readthrough in many physiological and disease conditions remains to be explored. RESULTS: To facilitate a wider investigation into transcriptional readthrough, we created the DoGFinder software package, for the streamlined identification and quantification of readthrough transcripts, also known as DoGs (Downstream of Gene-containing transcripts), from any RNA-seq dataset. Using DoGFinder, we explore the dependence of DoG discovery potential on RNA-seq library depth, and show that stress-induced readthrough induction discovery is robust to sequencing depth, and input parameter settings. We further demonstrate the use of the DoGFinder software package on a new publically available RNA-seq dataset, and discover DoG induction in human PME cells following hypoxia - a previously unknown readthrough inducing stress type. CONCLUSIONS: DoGFinder will enable users to explore, in a few simple steps, the readthrough phenomenon in any condition and organism. DoGFinder is freely available at https://github.com/shalgilab/DoGFinder .
Assuntos
Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Software , Animais , Hipóxia Celular , Células Endoteliais/citologia , Regulação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Pulmão/irrigação sanguínea , Microvasos/citologiaRESUMO
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.
Assuntos
Biodiversidade , Magnoliopsida/fisiologia , Filogenia , Simulação por Computador , Bases de Dados como Assunto , Probabilidade , Característica Quantitativa Herdável , ReproduçãoRESUMO
PREMISE OF THE STUDY: Flowering plants display a variety of sexual systems, ranging from complete cosexuality (hermaphroditism) to separate-sexed individuals (dioecy). While dioecy is relatively rare, it has evolved many times and is present in many plant families. Transitions in sexual systems are hypothesized to be affected by large genomic events such as whole-genome duplication, or polyploidy, and several models have been proposed to explain the observed patterns of association. METHODS: In this study, we assessed the association between ploidy and sexual system (separate or combined sexes). To this end, we assembled a database of ploidy levels and sexual systems for â¼1000 species, spanning 18 genera and 15 families. We applied several phylogenetic comparative approaches, including Pagel's coevolutionary framework and sister clade analyses, for detecting correlations between ploidy level and sexual system. KEY RESULTS: Our results indicate a broad association between polyploidy and sexual system dimorphism, with low evolutionary stability of the diploid-dioecious condition observed in several clades. A detailed examination of the clades exhibiting this correlation reveals that it is underlain by various patterns of transition rate asymmetry. CONCLUSIONS: We conclude that the long-hypothesized connection between ploidy and sexual system holds in some clades, although it may well be affected by factors that differ from clade to clade. Our results further demonstrate that to better understand the evolutionary processes involved, more sophisticated methods and extensive and detailed data sets are required for both broad and focused inquiry.
Assuntos
Genoma de Planta/genética , Magnoliopsida/genética , Modelos Genéticos , Poliploidia , Evolução Biológica , Diploide , Filogenia , Reprodução/genéticaRESUMO
Cancers that are poorly immune infiltrated pose a substantial challenge, with current immunotherapies yielding limited clinical success. Stem-like memory T cells (TSCM) have been identified as a subgroup of T cells that possess strong proliferative capacity and that can expand and differentiate following interactions with dendritic cells (DCs). In this study, we explored the pattern of expression of a recently discovered inhibitory receptor poliovirus receptor-related immunoglobulin domain protein (PVRIG) and its ligand, poliovirus receptor-related ligand 2 (PVRL2), in the human tumor microenvironment. Using spatial and single-cell RNA transcriptomics data across diverse cancer indications, we found that among the T-cell checkpoints, PVRIG is uniquely expressed on TSCM and PVRL2 is expressed on DCs in immune aggregate niches in tumors. PVRIG blockade could therefore enhance TSCM-DC interactions and efficiently drive T-cell infiltration to tumors. Consistent with these data, following PVRIG blockade in patients with poorly infiltrated tumors, we observed immune modulation including increased tumor T-cell infiltration, T-cell receptor (TCR) clonality, and intratumoral T-cell expansion, all of which were associated with clinical benefit. These data suggest PVRIG blockade as a promising strategy to induce potent antitumor T-cell responses, providing a novel approach to overcome resistance to immunotherapy in immune-excluded tumors.
Assuntos
Células Dendríticas , Neoplasias , Microambiente Tumoral , Humanos , Células Dendríticas/imunologia , Células Dendríticas/metabolismo , Microambiente Tumoral/imunologia , Neoplasias/imunologia , Neoplasias/terapia , Neoplasias/metabolismo , Linfócitos do Interstício Tumoral/imunologia , Linfócitos do Interstício Tumoral/metabolismo , Células T de Memória/imunologia , Células T de Memória/metabolismo , Linfócitos T/imunologia , Linfócitos T/metabolismoRESUMO
New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been "overprinted" by a new open reading frame, a process that generates a new protein-coding gene overlapping the ancestral gene. We analyzed the evolution of 12 experimentally validated viral genes that originated de novo and estimated their relative ages. We found that young de novo genes have a different codon usage from the rest of the genome. They evolve rapidly and are under positive or weak purifying selection. Thus, young de novo genes might have strain-specific functions, or no function, and would be difficult to detect using current genome annotation methods that rely on the sequence signature of purifying selection. In contrast to young de novo genes, older de novo genes have a codon usage that is similar to the rest of the genome. They evolve slowly and are under stronger purifying selection. Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene.
Assuntos
Códon/genética , Evolução Molecular , Homologia de Genes/genética , Seleção Genética , Proteínas Virais/genética , Biologia Computacional , Variação GenéticaRESUMO
Mutational robustness describes the extent to which a phenotype remains unchanged in the face of mutations. Theory predicts that the strength of direct selection for mutational robustness is at most the magnitude of the rate of deleterious mutation. As far as nucleic acid sequences are concerned, only long sequences in organisms with high deleterious mutation rates and large population sizes are expected to evolve mutational robustness. Surprisingly, recent studies have concluded that molecules that meet none of these conditions--the microRNA precursors (pre-miRNAs) of multicellular eukaryotes--show signs of selection for mutational and/or environmental robustness. To resolve the apparent disagreement between theory and these studies, we have reconstructed the evolutionary history of Drosophila pre-miRNAs and compared the robustness of each sequence to that of its reconstructed ancestor. In addition, we "replayed the tape" of pre-miRNA evolution via simulation under different evolutionary assumptions and compared these alternative histories with the actual one. We found that Drosophila pre-miRNAs have evolved under strong purifying selection against changes in secondary structure. Contrary to earlier claims, there is no evidence that these RNAs have been shaped by either direct or congruent selection for any kind of robustness. Instead, the high robustness of Drosophila pre-miRNAs appears to be mostly intrinsic and likely a consequence of selection for functional structures.
Assuntos
Drosophila/genética , Evolução Molecular , MicroRNAs/genética , Penetrância , Algoritmos , Animais , Simulação por Computador , Mutação , Conformação de Ácido Nucleico , Filogenia , Seleção Genética , Estatísticas não ParamétricasRESUMO
An overlapping open reading frame (ORF) with a potential to encode a functional protein has been identified within the 3'-proximal ORF of Solenopsis invicta virus 1 (SINV-1) and three bee viruses. This ORF has been referred to as predicted overlapping gene (pog). Protein motif searches of POG revealed weak relationships precluding assignment of a potential function. Neither a transcript nor a protein encoded by the pog ORF has been detected. However, recently, a protein encoded by the corresponding +1 overlapping ORF (termed ORFx) in the Israeli acute paralysis virus (IAPV) was demonstrated by recombinant means as well as in IAPV-infected honey bees. The objective of our study was to attempt to provide empirical evidence for the presence of a pog-derived protein from SINV-1-infected fire ants. A number of different laboratory and field SINV-1-infected Solenopsis invicta preparations were examined by western blotting for the presence of a POG protein sequence. In every case, these preparations failed to yield any detectable bands when probed with a polyclonal antibody preparation raised to a portion of the pog predicted protein sequence. Although impossible to prove a negative result, proper controls used in these studies suggested that the pog ORF is not translated into a functional protein in SINV-1.
Assuntos
Dicistroviridae/metabolismo , Homologia de Genes , Biossíntese de Proteínas , Proteínas Virais/metabolismo , Animais , Formigas/virologia , Abelhas/virologia , Dicistroviridae/genética , Vírus de Insetos/genética , Vírus de Insetos/metabolismo , Fases de Leitura Aberta/genética , Fases de Leitura Aberta/fisiologia , Análise de Sequência de DNA , Proteínas Virais/genéticaRESUMO
Protein-coding genes often contain long overlapping open-reading frames (ORFs), which may or may not be functional. Current methods that utilize the signature of purifying selection to detect functional overlapping genes are limited to the analysis of sequences from divergent species, thus rendering them inapplicable to genes found only in closely related sequences. Here, we present a method for the detection of selection signatures on overlapping reading frames by using closely related sequences, and apply the method to several known overlapping genes, and to an overlapping ORF on the negative strand of segment 8 of influenza A virus (NEG8), for which the suggestion has been made that it is functional. We find no evidence that NEG8 is under selection, suggesting that the intact reading frame might be non-functional, although we cannot fully exclude the possibility that the method is not sensitive enough to detect the signature of selection acting on this gene. We present the limitations of the method using known overlapping genes and suggest several approaches to improve it in future studies. Finally, we examine alternative explanations for the sequence conservation of NEG8 in the absence of selection. We show that overlap type and genomic context affect the conservation of intact overlapping ORFs and should therefore be considered in any attempt of estimating the signature of selection in overlapping genes.
Assuntos
Homologia de Genes , Vírus da Influenza A/genética , Influenza Humana/genética , Seleção Genética , Proteínas Virais/genética , Vírus/genética , Algoritmos , Genoma Viral , Humanos , Influenza Humana/virologia , Mutação , Filogenia , Fases de Leitura/genéticaRESUMO
As far as protein-coding genes are concerned, there is a non-zero probability that at least one of the five possible overlapping sequences of any gene will contain an open-reading frame (ORF) of a length that may be suitable for coding a functional protein. It is, however, very difficult to determine whether or not such an ORF is functional. Recently, we proposed a method that predicts functionality of an overlapping ORF if it can be shown that it has been subject to purifying selection during its evolution. Here, we use simulation to test this method under several conditions and compare it with the method of Firth and Brown. We found that under most conditions, our method detects functional overlapping genes with higher sensitivity than Firth and Brown's method, while maintaining high specificity. Further, we tested the hypothesis that the two aminoacyl tRNA synthetase classes have originated from a pair of overlapping genes. A central piece of evidence ostensibly supporting this hypothesis is the assertion that an overlapping ORF of a heat-shock protein-70 gene, which exhibits some similarity to class 2 aminoacyl tRNA synthetases, is functional. We found signature of purifying selection only in highly divergent sequences, suggesting that the method yields false-positives in high sequence divergence and that the overlapping ORF is not a functional gene. Finally, we examined three cases of overlap in the human genome. We find varying signatures of purifying selection acting on these overlaps, raising the possibility that two of the overlapping genes may not be functional.
Assuntos
Simulação por Computador , Homologia de Genes/genética , Animais , DNA Antissenso/genética , Genoma Humano/genética , Humanos , Camundongos , Fases de Leitura Aberta/genética , Seleção GenéticaRESUMO
The Israeli acute paralysis virus (IAPV) is a honeybee-infecting virus that was found to be associated with colony collapse disorder. The IAPV genome contains two genes encoding a structural and a nonstructural polyprotein. We applied a recently developed method for the estimation of selection in overlapping genes to detect purifying selection and, hence, functionality. We provide evolutionary evidence for the existence of a functional overlapping gene, which is translated in the +1 reading frame of the structural polyprotein gene. Conserved orthologs of this putative gene, which we provisionally call pog (predicted overlapping gene), were also found in the genomes of a monophyletic clade of dicistroviruses that includes IAPV, acute bee paralysis virus, Kashmir bee virus, and Solenopsis invicta (red imported fire ant) virus 1.
Assuntos
Homologia de Genes , Genoma Viral , Vírus de RNA/genética , Sequência de Aminoácidos , Dados de Sequência Molecular , Filogenia , Vírus de RNA/química , Vírus de RNA/classificação , Alinhamento de SequênciaRESUMO
The endoplasmic reticulum (ER) stress response, also known as the unfolded protein response (UPR), is a complex cellular response to ER protein misfolding that involves transcriptional regulatory branches and a PERK-mediated translational regulatory branch. Here we revealed that amino acid biosynthesis regulation is coupled to protein synthesis demands during ER stress. Specifically, we demonstrated that the UPR leads to PERK-dependent induction in the biosynthesis of specific amino acids, and to upregulation of their corresponding tRNA synthetases. Furthermore, we found that sequences of UPR-upregulated proteins are significantly enriched with these UPR-induced amino acids. Interestingly, whereas the UPR leads to repression of ER target proteins, we showed that secreted proteins tended to escape this repression and were highly enriched for the UPR-induced amino acids. Our results unravel coordination between amino acid supply, namely, biosynthesis and tRNA loading, and demand from UPR-induced proteins under ER stress, thus revealing an additional regulatory layer of protein synthesis.
RESUMO
The UPR (Unfolded Protein Response) is a well-orchestrated response to ER protein folding and processing overload, integrating both transcriptional and translational outputs. Its three arms in mammalian cells, the PERK translational response arm, together with the ATF6 and IRE1-XBP1-mediated transcriptional arms, have been thoroughly investigated. Using ribosome footprint profiling, we performed a deep characterization of gene expression programs involved in the early and late ER stress responses, within WT or PERK -/- Mouse Embryonic Fibroblasts (MEFs). We found that both repression and activation gene expression programs, affecting hundreds of genes, are significantly hampered in the absence of PERK. Specifically, PERK -/- cells do not show global translational inhibition, nor do they specifically activate early gene expression programs upon short exposure to ER stress. Furthermore, while PERK -/- cells do activate/repress late ER-stress response genes, the response is substantially weaker. Importantly, we highlight a widespread PERK-dependent repression program, consisting of ER targeted proteins, including transmembrane proteins, glycoproteins, and proteins with disulfide bonds. This phenomenon occurs in various different cell types, and has a major translational regulatory component. Moreover, we revealed a novel interplay between PERK and the XBP1-ATF6 arms of the UPR, whereby PERK attenuates the expression of a specific subset of XBP1-ATF6 targets, further illuminating the complexity of the integrated ER stress response.
Assuntos
Estresse do Retículo Endoplasmático/fisiologia , Retículo Endoplasmático/fisiologia , Resposta a Proteínas não Dobradas , eIF-2 Quinase/metabolismo , Fator 6 Ativador da Transcrição/metabolismo , Animais , Estresse do Retículo Endoplasmático/genética , Expressão Gênica , Células HEK293 , Humanos , Camundongos , Camundongos Knockout , Células NIH 3T3 , Biossíntese de Proteínas , Proteína 1 de Ligação a X-Box/metabolismo , eIF-2 Quinase/genéticaRESUMO
Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the uneven distribution of polyploid plants across the globe. Nevertheless, the lack of large comparative datasets has restricted such studies to local floras and to narrow taxonomical scopes, limiting our understanding of the underlying drivers of polyploid plant distribution. We present a map portraying the worldwide polyploid frequencies, based on extensive spatial data coupled with phylogeny-based polyploidy inference for tens of thousands of species. This allowed us to assess the potential global drivers affecting polyploid distribution. Our data reveal a clear latitudinal trend, with polyploid frequency increasing away from the equator. Climate, especially temperature, appears to be the most influential predictor of polyploid distribution. However, we find this effect to be mostly indirect, mediated predominantly by variation in plant lifeforms and, to a lesser extent, by taxonomical composition and species richness. Thus, our study presents an emerging view of polyploid distribution that highlights attributes that facilitate the establishment of new polyploid lineages by providing polyploids with sufficient time (that is, perenniality) and space (low species richness) to compete with pre-adapted diploid relatives.
Assuntos
Evolução Biológica , Filogeografia , Plantas/genética , Poliploidia , FlorestasRESUMO
Systemic RNAi, initiated by double-stranded RNA (dsRNA) ingestion, has been reported in diverse invertebrates, including honey bees, demonstrating environmental RNA uptake that undermines homologous gene expression. However, the question why any organism would take up RNA from the environment has remained largely unanswered. Here, we report on horizontal RNA flow among honey bees mediated by secretion and ingestion of worker and royal jelly diets. We demonstrate that transmission of jelly-secreted dsRNA to larvae is biologically active and triggers gene knockdown that lasts into adulthood. Worker and royal jellies harbor differential naturally occurring RNA populations. Jelly RNAs corresponded to honey bee protein-coding genes, transposable elements, and non-coding RNA, as well as bacteria, fungi, and viruses. These results reveal an inherent property of honey bees to share RNA among individuals and generations. Our findings suggest a transmissible RNA pathway, playing a role in social immunity and signaling between members of the hive.
Assuntos
Abelhas/genética , Interferência de RNA/fisiologia , RNA de Cadeia Dupla/genética , Transdução de Sinais/genética , Animais , Ácidos Graxos/genética , Ácidos Graxos/fisiologia , Transferência Genética Horizontal/fisiologia , Larva/genética , Larva/metabolismo , Larva/fisiologia , RNA de Cadeia Dupla/fisiologiaRESUMO
Sexual system is a key determinant of genetic variation and reproductive success, affecting evolution within populations and within clades. Much research in plants has focused on evolutionary transitions away from the most common state of hermaphroditism and toward the rare state of dioecy (separate sexes). Rather than transitions predominantly toward greater sexual differentiation, however, evolution may proceed in the direction of lesser sexual differentiation. We analyzed the macroevolutionary dynamics of sexual system in angiosperm genera that contain both dioecious and nondioecious species. Our phylogenetic analyses encompass a total of 2145 species from 40 genera. Overall, we found little evidence that rates of sexual system transitions are greater in any direction. Counting the number of inferred state changes revealed a mild prevalence of transitions away from hermaphroditism and away from dioecy, toward states of intermediate sexual differentiation. We identify genera in which future studies of sexual system evolution might be especially productive, and we discuss how integrating genetic or population-level studies of sexual system could improve the power of phylogenetic comparative analyses. Our work adds to the evidence that different selective pressures and constraints act in different groups, helping maintain the variety of sexual systems observed among plants.
Assuntos
Evolução Biológica , Magnoliopsida/fisiologia , Filogenia , Variação Genética , Magnoliopsida/genética , ReproduçãoRESUMO
Polyploidy is commonly thought to be associated with the domestication process because of its concurrence with agriculturally favourable traits and because it is widespread among the major plant crops(1-4). Furthermore, the genetic consequences of polyploidy(5-7) might have increased the adaptive plasticity of those plants, enabling successful domestication(6-8). Nevertheless, a detailed phylogenetic analysis regarding the association of polyploidy with the domestication process, and the temporal order of these distinct events, has been lacking(3). Here, we have gathered a comprehensive data set including dozens of genera, each containing one or more major crop species and for which sufficient sequence and chromosome number data exist. Using probabilistic inference of ploidy levels conducted within a phylogenetic framework, we have examined the incidence of polyploidization events within each genus. We found that domesticated plants have gone through more polyploidy events than their wild relatives, with monocots exhibiting the most profound difference: 54% of the crops are polyploids versus 40% of the wild species. We then examined whether the preponderance of polyploidy among crop species is the result of two, non-mutually-exclusive hypotheses: (1) polyploidy followed by domestication, and (2) domestication followed by polyploidy. We found support for the first hypothesis, whereby polyploid species were more likely to be domesticated than their wild relatives, suggesting that the genetic consequences of polyploidy have conferred genetic preconditions for successful domestication on many of these plants.
Assuntos
Produtos Agrícolas/genética , Domesticação , Duplicação Gênica , Genoma de Planta , PoliploidiaRESUMO
[This corrects the article DOI: 10.1002/ece3.2277.].