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1.
Plant J ; 116(6): 1842-1855, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37665679

RESUMO

Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby Strobilanthes. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated a full-length transcriptome resource incorporated into the BlueOmics database (http://blueomics.iflora.cn) for two Strobilanthes species, which feature contrasting flowering time behaviors. Using about 112 and 104 Gb Iso-seq reads together with ~185 and ~75 Gb strand-specific RNA seq data, we annotated 80 971 and 79 985 non-redundant full-length transcripts for the perennial polycarpic Strobilanthes tetrasperma and the perennial monocarpic Strobilanthes biocullata, respectively. In S. tetrasperma, we identified 8794 transcripts showing spatiotemporal expression in nine tissues. In leaves and shoot apical meristems at two developmental stages, 977 and 1121 transcripts were differentially accumulated in S. tetrasperma and S. biocullata, respectively. Interestingly, among the 33 transcription factors showing differential expression in S. tetrasperma but without differential expression in S. biocullata, three were involved potentially in the photoperiod and circadian-clock pathway of flowering time regulation (FAR1 RELATED SEQUENCE 12, FRS12; NUCLEAR FACTOR Y A1, NFYA1; PSEUDO-RESPONSE REGULATOR 5, PRR5), hence provides an important clue in deciphering the flowering diversity mechanisms. Our data serve as a key resource for further dissection of molecular and genetic mechanisms underpinning key biological innovations, here, the perennial monocarpic mass flowering.


Assuntos
Flores , Transcriptoma , Humanos , Transcriptoma/genética , Flores/genética , Flores/metabolismo , Perfilação da Expressão Gênica , Folhas de Planta/metabolismo , RNA-Seq , Regulação da Expressão Gênica de Plantas/genética
2.
Plant Physiol ; 192(1): 154-169, 2023 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-36721922

RESUMO

Flowering transition is tightly coordinated by complex gene regulatory networks, in which AGAMOUS-LIKE 16 (AGL16) plays important roles. Here, we identified the molecular function and binding properties of AGL16 and demonstrated its partial dependency on the SUPPRESSOR OF CONSTANS 1 (SOC1) function in regulating flowering. AGL16 bound to promoters of more than 2,000 genes via CArG-box motifs with high similarity to that of SOC1 in Arabidopsis (Arabidopsis thaliana). Approximately 70 flowering genes involved in multiple pathways were potential targets of AGL16. AGL16 formed a protein complex with SOC1 and shared a common set of targets. Intriguingly, only a limited number of genes were differentially expressed in the agl16-1 loss-of-function mutant. However, in the soc1-2 knockout background, AGL16 repressed and activated the expression of 375 and 182 genes, respectively, with more than a quarter bound by AGL16. Corroborating these findings, AGL16 repressed the flowering time more strongly in soc1-2 than in the Col-0 background. These data identify a partial inter-dependency between AGL16 and SOC1 in regulating genome-wide gene expression and flowering time, while AGL16 provides a feedback regulation on SOC1 expression. Our study sheds light on the complex background dependency of AGL16 in flowering regulation, thus providing additional insights into the molecular coordination of development and environmental adaptation.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Proteínas de Domínio MADS/genética , Proteínas de Domínio MADS/metabolismo , Regiões Promotoras Genéticas/genética , Regulação da Expressão Gênica de Plantas , Flores
3.
J Exp Bot ; 75(11): 3233-3247, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38546444

RESUMO

Floral forms with an increased number of petals, also known as double-flower phenotypes, have been selected and conserved in many domesticated plants, particularly in ornamentals, because of their great economic value. The molecular and genetic mechanisms that control this trait are therefore of great interest, not only for scientists, but also for breeders. In this review, we summarize current knowledge of the gene regulatory networks of flower initiation and development and known mutations that lead to variation of petal number in many species. In addition to the well-accepted miR172/AP2-like module, for which many questions remain unanswered, we also discuss other pathways in which mutations also lead to the formation of extra petals, such as those involved in meristem maintenance, hormone signalling, epigenetic regulation, and responses to environmental signals. We discuss how the concept of 'natural mutants' and recent advances in genomics and genome editing make it possible to explore the molecular mechanisms underlying double-flower formation, and how such knowledge could contribute to the future breeding and selection of this trait in more crops.


Assuntos
Flores , Flores/genética , Flores/crescimento & desenvolvimento , Flores/anatomia & histologia , Regulação da Expressão Gênica de Plantas , Mutação , Redes Reguladoras de Genes
4.
J Exp Bot ; 75(13): 3946-3958, 2024 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-38642399

RESUMO

Plant life history is determined by two transitions, germination and flowering time, in which the phosphatidylethanolamine-binding proteins (PEBPs) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) play key regulatory roles. Compared with the highly conserved TFL1-like genes, FT-like genes vary significantly in copy numbers in gymnosperms, and monocots within the angiosperms, while sporadic duplications can be observed in eudicots. Here, via a systematic analysis of the PEBPs in angiosperms with a special focus on 12 representative species featuring high-quality genomes in the order Lamiales, we identified a successive lineage-specific but systematic expansion of FT-like genes in the families of core Lamiales. The first expansion event generated FT1-like genes mainly via a core Lamiales-specific whole-genome duplication (cL-WGD), while a likely random duplication produced the FT2-like genes in the lineages containing Scrophulariaceae and the rest of the core Lamiales. Both FT1- and FT2-like genes were further amplified tandemly in some families. These expanded FT-like genes featured highly diverged expression patterns and structural variation, indicating functional diversification. Intriguingly, some core Lamiales contained the relict MOTHER OF FT AND TFL1 like 2 (MFT2) that probably expanded in the common ancestor of angiosperms. Our data showcase the highly dynamic lineage-specific expansion of the FT-like genes, and thus provide important and fresh evolutionary insights into the gene regulatory network underpinning flowering time diversity in Lamiales and, more generally, in angiosperms.


Assuntos
Evolução Molecular , Magnoliopsida , Filogenia , Proteínas de Plantas , Magnoliopsida/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteína de Ligação a Fosfatidiletanolamina/genética , Proteína de Ligação a Fosfatidiletanolamina/metabolismo , Flores/genética , Flores/crescimento & desenvolvimento , Duplicação Gênica
5.
Plant Cell Rep ; 43(2): 36, 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38200362

RESUMO

KEY MESSAGE: Detailed analyses of 16 genomes identified a remarkable acceleration of mutation rate, hence mitochondrial sequence and structural heterogeneity, in Meniocus linifolius (Brassicaceae). The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newly assembled and 13 known mitochondrial genomes (mitogenomes), we report the highly variable genome structure and mutation rates in Brassicaceae. The genome sizes and GC contents are 196,604 bp and 46.83%, 288,122 bp and 44.79%, and 287,054 bp and 44.93%, for Meniocus linifolius (Mli), Crucihimalaya lasiocarpa (Cla), and Lepidium sativum (Lsa), respectively. In total, 29, 33, and 34 protein-coding genes (PCGs) and 14, 18, and 18 tRNAs are annotated for Mli, Cla, and Lsa, respectively, while all mitogenomes contain one complete circular molecule with three rRNAs and abundant RNA editing sites. The Mli mitogenome features four conformations likely mediated by the two pairs of long repeats, while at the same time seems to have an unusual evolutionary history due to higher GC content, loss of more genes and sequences, but having more repeats and plastid DNA insertions. Corroborating with these, an ambiguous phylogenetic position with long branch length and elevated synonymous substitution rate in nearly all PCGs are observed for Mli. Taken together, our results reveal a high level of mitogenome heterogeneity at the family level and provide valuable resources for further understanding the evolutionary pattern of organelle genomes in Brassicaceae.


Assuntos
Brassicaceae , Genoma Mitocondrial , Genoma Mitocondrial/genética , Brassicaceae/genética , Filogenia , Evolução Biológica , DNA Mitocondrial/genética
6.
BMC Plant Biol ; 21(1): 204, 2021 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-33910529

RESUMO

BACKGROUND: The Rhododendron sanguineum complex is endemic to alpine mountains of northwest Yunnan and southeast Tibet of China. Varieties in this complex exhibit distinct flower colors even at the bud stage. However, the underlying molecular regulations for the flower color variation have not been well characterized. Here, we investigated this via measuring flower reflectance profiles and comparative transcriptome analyses on three coexisting varieties of the R. sanguineum complex, with yellow flush pink, bright crimson, and deep blackish crimson flowers respectively. We compared the expression levels of differentially-expressed-genes (DEGs) of the anthocyanin / flavonoid biosynthesis pathway using RNA-seq and qRT-PCR data. We performed clustering analysis based on transcriptome-derived Single Nucleotide Polymorphisms (SNPs) data, and finally analyzed the promoter architecture of DEGs. RESULTS: Reflectance spectra of the three color morphs varied distinctively in the range between 400 and 700 nm, with distinct differences in saturation, brightness, hue, and saturation/hue ratio, an indirect measurement of anthocyanin content. We identified 15,164 orthogroups that were shared among the three varieties. The SNP clustering analysis indicated that the varieties were not monophyletic. A total of 40 paralogous genes encoding 12 enzymes contributed to the flower color polymorphism. These anthocyanin biosynthesis-related genes were associated with synthesis, modification and transportation properties (RsCHS, RsCHI, RsF3H, RsF3'H, RsFLS, RsANS, RsAT, RsOMT, RsGST), as well as genes involved in catabolism and degradation (RsBGLU, RsPER, RsCAD). Variations in sequence and cis-acting elements of these genes might correlate with the anthocyanin accumulation, thus may contribute to the divergence of flower color in the R. sanguineum complex. CONCLUSIONS: Our results suggested that the varieties are very closely related and flower color variations in the R. sanguineum complex correlate tightly with the differential expression levels of genes involved in the anabolic and catabolic synthesis network of anthocyanin. Our study provides a scenario involving intricate relationships between genetic mechanisms for floral coloration accompanied by gene flow among the varieties that may represent an early case of pollinator-mediated incipient sympatric speciation.


Assuntos
Antocianinas/metabolismo , Flavonoides/metabolismo , Proteínas de Plantas/genética , Polimorfismo de Nucleotídeo Único/genética , Rhododendron/genética , Transcriptoma , Cor , Flores/genética , Flores/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Fluxo Gênico , Especiação Genética , Pigmentação/genética , Rhododendron/metabolismo , Simpatria , Tibet
8.
Plant Mol Biol ; 104(1-2): 81-95, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32621166

RESUMO

KEY MESSAGE: Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.


Assuntos
Genes de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Rosaceae/genética , Rosaceae/metabolismo , Ubiquitina-Proteína Ligases/genética , Sequência de Aminoácidos , Arabidopsis/genética , Arabidopsis/metabolismo , Cromossomos de Plantas/genética , Domesticação , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Filogenia , Plantas Geneticamente Modificadas , Rosa/genética , Rosa/metabolismo , Ubiquitina-Proteína Ligases/metabolismo
9.
Opt Express ; 27(13): 19002-19018, 2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31252834

RESUMO

The fluorescence enhancement in an over-etched gold zero-mode waveguide (ZMW) was investigated through both numerical simulation and experiments. Using Cy3 and Cy5 as the fluorescent probes, the simulation showed that the undercut not only enhances the fluorescence signals of both fluorophores, but also greatly improves the radial uniformity of the excitation fields in the ZMW. Furthermore, using a focused-ion-beam tool, we fabricated Au-ZMW arrays with different radius and undercut. The fluorescence enhancement per molecule and the effective excitation volume of the Au-ZMW were then measured as functions of its radial size and over-etching depth by using fluorescence correlation spectroscopy. It was found that the undercut can significantly enhance the fluorescence signal per molecule in the ZMW, but it also slightly increased the excitation volume. Decreasing the radial size of the ZMW can efficiently reduce the excitation volume and also further enhance the fluorescence per molecule. These results together indicate that combining the undercut and reduction of radius of the ZMW can serve as a simple and effective way to essentially improve the performance of an Au-ZMW for single molecule fluorescence detection.

10.
BMC Plant Biol ; 18(1): 371, 2018 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-30579326

RESUMO

BACKGROUND: Roses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge. RESULTS: Here, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis 'Old Blush' (OB) and R. wichuriana 'Basye's Thornless' (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes. CONCLUSIONS: We expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.


Assuntos
Rosa/genética , Seleção Genética/genética , Transcriptoma/genética , Perfilação da Expressão Gênica , Genes de Plantas/genética , Hibridização Genética/genética , Filogenia , Rosácea/genética , Análise de Sequência de DNA
11.
Plant Cell ; 26(5): 2024-2037, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24876250

RESUMO

The timing of flowering is pivotal for maximizing reproductive success under fluctuating environmental conditions. Flowering time is tightly controlled by complex genetic networks that integrate endogenous and exogenous cues, such as light, temperature, photoperiod, and hormones. Here, we show that AGAMOUS-LIKE16 (AGL16) and its negative regulator microRNA824 (miR824) control flowering time in Arabidopsis thaliana. Knockout of AGL16 effectively accelerates flowering in nonvernalized Col-FRI, in which the floral inhibitor FLOWERING LOCUS C (FLC) is strongly expressed, but shows no effect if plants are vernalized or grown in short days. Alteration of AGL16 expression levels by manipulating miR824 abundance influences the timing of flowering quantitatively, depending on the expression level and number of functional FLC alleles. The effect of AGL16 is fully dependent on the presence of FLOWERING LOCUS T (FT). Further experiments show that AGL16 can interact directly with SHORT VEGETATIVE PHASE and indirectly with FLC, two proteins that form a complex to repress expression of FT. Our data reveal that miR824 and AGL16 modulate the extent of flowering time repression in a long-day photoperiod.

12.
BMC Genomics ; 17: 382, 2016 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-27206349

RESUMO

BACKGROUND: Pseudostellaria heterophylla produces both closed (cleistogamous, CL) and open (chasmogamous, CH) flowers on the same individual but in different seasons. The production of CH and CL flowers might be in response to environmental changes. To better understand the molecular mechanisms of CH and CL flowering, we compared the transcriptome of the two types of flowers to examine differential gene expression patterns, and to identify gene regulatory networks that control CH and CL flowering. RESULTS: Using RNA sequencing, we identified homologues of 428 Arabidopsis genes involved in regulating flowering processes and estimated the differential gene expression patterns between CH and CL flowers. Some of these genes involved in gene regulatory networks of flowering processes showed significantly differential expression patterns between CH and CL flowers. In addition, we identified another 396 differentially expressed transcripts between CH and CL flowers. Some are involved in environmental stress responses and flavonoid biosynthesis. CONCLUSIONS: We propose how the differential expression of key members of three gene regulatory modules may explain CH and CL flowering. Future research is needed to investigate how the environment impinges on these flowering pathways to regulate CH and CL flowering in P. heterophylla.


Assuntos
Caryophyllaceae/genética , Flores/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Biologia Computacional/métodos , Meio Ambiente , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Modelos Biológicos , Anotação de Sequência Molecular , Fenótipo , Reprodutibilidade dos Testes , Transcriptoma
13.
ScientificWorldJournal ; 2014: 837586, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25133262

RESUMO

Three-dimensional (3D) backside reflector, compared with flat reflectors, can improve the probability of finding the escape cone for reflecting lights and thus enhance the light-extraction efficiency (LEE) for GaN-based light-emitting diode (LED) chips. A triangle-lattice of microscale SiO2 cone array followed by a 16-pair Ti3O5/SiO2 distributed Bragg reflector (16-DBR) was proposed to be attached on the backside of sapphire substrate, and the light-output enhancement was demonstrated by numerical simulation and experiments. The LED chips with flat reflectors or 3D reflectors were simulated using Monte Carlo ray tracing method. It is shown that the LEE increases as the reflectivity of backside reflector increases, and the light-output can be significantly improved by 3D reflectors compared to flat counterparts. It can also be observed that the LEE decreases as the refractive index of the cone material increases. The 3D 16-DBR patterned by microscale SiO2 cone array benefits large enhancement of LEE. This microscale pattern was prepared by standard photolithography and wet-etching technique. Measurement results show that the 3D 16-DBR can provide 12.1% enhancement of wall-plug efficiency, which is consistent with the simulated value of 11.73% for the enhancement of LEE.


Assuntos
Eletrônica/instrumentação , Gálio/química , Iluminação/instrumentação , Iluminação/métodos , Dióxido de Silício/química , Titânio/química
14.
ACS Sens ; 9(6): 3126-3136, 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38843033

RESUMO

Given the widespread utilization of gas sensors across various industries, the detection of diverse and complex target gases presents a significant challenge in designing sensors with multigas detection capability. Although constructing a sensor array with widely used chemiresistive gas sensors is one solution, it is difficult for a single chemiresistive gas sensor to simultaneously detect different gases, as it can only detect a single target gas. The intrinsic reason for this bottleneck is that chemiresistive gas sensors rely entirely on the resistivity as the unique parameter to evaluate the diverse gas sensing properties of sensors, such as sensitivity, selectivity, etc. Herein, a field-effect transistor (FET) with abundant electrical parameters is employed to prepare a gas sensor for the detection of a variety of gases. Semiconducting carbon nanotubes (CNTs) are selected as the channel material, which is modified by Pd nanoparticles to enhance the gas sensing properties of the sensors. By extracting various electrical parameters such as transconductance, threshold voltage, etc. from the transfer characteristic curves of FET, a correlation between multielectrical parameters and various gas detection information is established for subsequent data analysis. Through the utilization of the principal component analysis algorithm, the identification of six gases can be finally achieved by relying solely on a single carbon-based FET-type gas sensor. We hope our work can solve the bottleneck of multigas identification by a single sensor in principle and is expected to reduce the system complexity and cost caused by the design of sensor arrays, offering a valuable guidance for multigas identification technology.


Assuntos
Gases , Nanotubos de Carbono , Transistores Eletrônicos , Nanotubos de Carbono/química , Gases/análise , Gases/química
15.
Plant Commun ; 5(7): 100878, 2024 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-38475995

RESUMO

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.


Assuntos
Brassicaceae , Genoma de Planta , Cariótipo , Filogenia , Brassicaceae/genética , Evolução Molecular , Cromossomos de Plantas/genética
16.
Mol Biol Evol ; 29(11): 3385-95, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-22641789

RESUMO

Cis-regulatory DNA has been suspected to play a preeminent role in adaptive evolution, but understanding the role of cis-regulatory mutations in gene expression divergence first requires an accurate analysis of the functional differences associated with these regions. We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species Arabidopsis thaliana and A. lyrata with a whole-genome SNP (single nucleotide polymorphism) tiling array. We observed 2,205 genes showing ASE pattern in at least one tissue. Nearly 90% of genes displaying ASE preferentially expressed the allele of A. lyrata. Genome-wide comparison of sequence divergence revealed that genes displaying ASE had a higher ratio of nonsynonymous to synonymous substitutions in coding regions. We further observe that the epigenetic landscape of histone methylation in A. thaliana genome associate with ASE. The asymmetry in the direction of allele-specific expression suggests interspecific differences in the efficiency of gene silencing in F1 hybrids.


Assuntos
Arabidopsis/genética , Variação Genética , Genoma de Planta/genética , Sequências Reguladoras de Ácido Nucleico/genética , Alelos , Substituição de Aminoácidos/genética , Cruzamentos Genéticos , Epigênese Genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Hibridização Genética , Modelos Genéticos , Análise de Sequência com Séries de Oligonucleotídeos , Especificidade de Órgãos/genética , Polimorfismo de Nucleotídeo Único , Reprodutibilidade dos Testes , Especificidade da Espécie
17.
Mol Biol Evol ; 29(3): 1081-91, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22086904

RESUMO

Transposable elements (TEs) are so abundant and variable that they count among the most important mutational sources in genomes. Nonetheless, little is known about the genetics of their variation in activity or silencing across closely related species. Here, we demonstrate that regulation of TE genes can differ dramatically between the two closely related Arabidopsis species A. thaliana and A. lyrata. In leaf and floral tissues of F1 interspecific hybrids, about 47% of TEs show allele-specific expression, with the A. lyrata copy being generally expressed at higher level. We confirm that TEs are generally expressed in A. lyrata but not in A. thaliana. Allele-specific differences in TE expression are associated with divergence in epigenetic modifications like DNA and histone methylation between species as well as with sequence divergence. Our data demonstrate that A. thaliana silences TEs much better than A. lyrata. For long terminal repeat retrotransposons, these differences are more pronounced for younger insertions. Interspecific differences in TE silencing may have a great impact on genome size changes.


Assuntos
Arabidopsis/genética , Elementos de DNA Transponíveis/genética , Regulação da Expressão Gênica de Plantas/genética , Imunoprecipitação da Cromatina , Biologia Computacional , Cruzamentos Genéticos , Flores/metabolismo , Genômica , Análise em Microsséries , Folhas de Planta/metabolismo , Especificidade da Espécie
18.
Nanoscale ; 14(47): 17550-17560, 2022 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-36318052

RESUMO

Dimer optical antennas (OAs) enable great fluorescence enhancement and excitation volume reduction and hence potentially can be a very useful tool for single-molecule detection. The realization of broadband fluorescence enhancement with a dimer OA remains an essential step for its usage in multi-color single-molecule fluorescence (SMF) detection. Although silver dimer OAs have been shown to be able to yield broadband fluorescence enhancement over the visible spectrum, they are amenable to oxidization, hard to functionalize, and could cause cytotoxicity. To overcome these limitations, in this work, we took advantage of nano-sized silver due to its optical properties and gold due to its chemical properties and developed an ameliorated Ag@Au dimer OA in terms of its overall performance. The Ag@Au nanoparticle in the dimer OA contains a 70 nm silver core and an ultra-thin (∼1-5 nm) gold shell which play a key role in its optical responses. Furthermore, we employed three typical dyes, i.e., FAM, TAMRA and Cy5, representing the blue, yellow and red ranges, respectively, and characterized their single-molecule fluorescence enhancements in the presence of Au or Ag@Au OAs. Our results indicate that, in contrast to its Au counterpart, the Ag@Au dimer OA prepared here can greatly improve its optical response in the blue range and eventually achieve broadband fluorescence enhancement throughout almost the whole visible spectral range. Meanwhile, it also maintains good chemical stability and accessibility to functionalization. Such Ag@Au dimer OAs are thus expected to have many important applications in the future, including single-molecule sequencing and multi-color biosensing.


Assuntos
Nanopartículas Metálicas , Prata , Ouro
19.
Hortic Res ; 92022 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-35031798

RESUMO

While roses are today among the most popular ornamental plants, the petals and fruits of some cultivars have flavored foods for millennia. The genetic origins of these edible cultivars remain poorly investigated. We collected the major varieties of edible roses available in China, assembled their plastome sequences, and phased the haplotypes for internal transcribed spacers (ITS1/ITS2) of the 18S-5.8S-26S nuclear ribosomal cistron. Our phylogenetic reconstruction using 88 plastid genomes, of primarily maternal origin, uncovered well-supported genetic relationships within Rosa, including all sections and all subgenera. We phased the ITS sequences to identify potential donor species ancestral to the development of known edible cultivars. The tri-parental Middle-Eastern origin of R. × damascena, the species most widely used in perfume products and food additives, was confirmed as a descendent of past hybridizations among R. moschata, R. gallica, and R. majalis/R. fedtschenkoana/R. davurica. In contrast, R. chinensis, R. rugosa, and R. gallica, in association with six other wild species, were the main donors for fifteen varieties of edible roses. The domesticated R. rugosa 'Plena' was shown to be a hybrid between R. rugosa and R. davurica, sharing a common origin with R. 'Fenghua'. Only R. 'Jinbian' and R. 'Crimson Glory' featured continuous flowering. All remaining cultivars of edible roses bloomed only once a year. Our study provides important resources for clarifying the origin of edible roses and suggests a future for breeding new cultivars with unique traits, such as continuous flowering.

20.
Proc Natl Acad Sci U S A ; 105(26): 8994-9, 2008 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-18579782

RESUMO

In plants and animals, gene expression can be down-regulated at the posttranscriptional level by microRNAs (miRNAs), a class of small endogenous RNA. Comparative analysis of miRNA content across species indicates continuous birth and death of these loci in the course of evolution. However, little is known about the microevolutionary dynamics of these genetic elements, especially in plants. In this article we examine polymorphism at two miRNA-encoding loci in Arabidopsis thaliana, miR856 and miR824, which are not found in rice or poplar. We compare their diversity to other miRNA-encoding loci conserved across distant taxa. We find that levels of variation vary significantly across loci and that the two recently derived loci harbor patterns of diversity deviating from neutrality. miRNA miR856 shows a weak signature of a selective sweep whereas miR824 displays signs of balancing selection. A detailed examination of structural variation among alleles found at the miR824-encoding locus suggests nonrandom evolution of a thermoresistant substructure in the precursor. Expression analysis of pre-miR824 and its target, AGL16, indicates that these structural differences likely impact the processing of mature miR824. Our work highlights the relevance of RNA structure in precursor sequence evolution, suggesting that the evolutionary dynamics of miRNA-encoding loci is more complex than suggested by the constraints exerted on the interaction between mature miRNA fragments and their target exon.


Assuntos
Alelos , Arabidopsis/genética , MicroRNAs/genética , Precursores de RNA/genética , RNA de Plantas/genética , Proteínas de Arabidopsis/genética , Regulação para Baixo , Evolução Molecular , Genes de Plantas , MicroRNAs/química , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Filogenia , Polimorfismo Genético , RNA de Plantas/química , Sequências Reguladoras de Ácido Nucleico/genética , Homologia de Sequência do Ácido Nucleico
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