RESUMEN
O-methyltransferases (OMTs) are a group of enzymes involved in several fundamental biological processes in plants, including lignin biosynthesis, pigmentation, and aroma production. Despite the intensive investigation of the role of OMTs in plant secondary metabolism, the evolution and diversification of this gene family in Solanaceae remain poorly understood. Here, we conducted a genome-wide survey of OMT genes in six Solanaceae species, reconstructing gene phylogenetic trees, predicting the potential involvement in biological processes, and investigating the exon/intron structure and chromosomal location. We identified 57 caffeoyl-CoA OMTs (CCoAOMTs) and 196 caffeic acid OMTs (COMTs) in the studied species. We observed a conserved gene block on chromosome 2 that consisted of tandem duplicated copies of OMT genes. Our results suggest that the expansion of the OMT gene family in Solanaceae was driven by whole genome duplication, segmental duplication, and tandem duplication, with multiple genes being retained by neofunctionalization and subfunctionalization. This study represents an essential first step in unraveling the evolutionary history of OMTs in Solanaceae. Our findings deepen our understanding of the crucial role of OMTs in several biological processes and highlight their significance as potential biotechnological targets.
RESUMEN
Plant RNases T2 are involved in several physiological and developmental processes, including inorganic phosphate starvation, senescence, wounding, defense against pathogens, and the self-incompatibility system. Solanaceae RNases form three main clades, one composed exclusively of S-RNases and two that include S-like RNases. We identified several positively selected amino acids located in highly flexible regions of these molecules, mainly close to the B1 and B2 substrate-binding sites in S-like RNases and the hypervariable regions of S-RNases. These differences between S- and S-like RNases in the flexibility of amino acids in substrate-binding regions are essential to understand the RNA-binding process. For example, in the S-like RNase NT, two positively selected amino acid residues (Tyr156 and Asn134) are located at the most flexible sites on the molecular surface. RNase NT is induced in response to tobacco mosaic virus infection; these sites may thus be regions of interaction with pathogen proteins or viral RNA. Differential selective pressures acting on plant ribonucleases have increased amino acid variability and, consequently, structural differences within and among S-like RNases and S-RNases that seem to be essential for these proteins play different functions.
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Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix-loop-helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.
Asunto(s)
Flores , Factores de Transcripción , Antocianinas , Flavonoides/genética , Flavonoides/metabolismo , Flores/genética , Regulación de la Expresión Génica de las Plantas , Pigmentación/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/metabolismo , Factores de Transcripción/metabolismoRESUMEN
Developmental genes are believed to contribute to major changes during plant evolution, from infrageneric to higher levels. Due to their putative high sequence conservation, developmental genes are rarely used as molecular markers, and few studies including these sequences at low taxonomic levels exist. WUSCHEL-related homeobox genes (WOX) are transcription factors exclusively present in plants and are involved in developmental processes. In this study, we characterized the infrageneric genetic variation of Petunia WOX genes. We obtained phylogenetic relationships consistent with other phylogenies based on nuclear markers, but with higher statistical support, resolution in terminals, and compatibility with flower morphological changes.
RESUMEN
The E2 promoter binding factor (E2F) proteins are present in almost all eukaryotic organisms and are essential to control several processes, such as the cell cycle progression, cell division, DNA replication, and apoptosis. The E2F family comprises two different types of proteins: the typical E2Fs and atypical E2Fs, which differ structurally and have specific functions. The E2F gene family was described for the first time in plants in 1999, and since then several studies have focused on the functional aspects, but the evolutionary history of this gene family is still unknown. Here, we investigated the evolutionary history of the E2F gene family in plants. Our findings suggest that E2F proteins arose early after the emergence of the eukaryotic species, while DEL proteins appear to have arisen before the metazoan and plants origin probably through a partial duplication of an ancient E2F protein. Our data also suggest that E2Fs activators and repressors appeared twice during evolution, once in the metazoan lineage and again in the embryophyte lineage.
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Proteínas de Unión al ADN/genética , Factores de Transcripción E2F/genética , Evolución Molecular , Proteínas de Plantas/genética , Viridiplantae/genética , Teorema de Bayes , Proteínas de Unión al ADN/clasificación , Bases de Datos de Proteínas , Factores de Transcripción E2F/clasificación , Filogenia , Proteínas de Plantas/clasificación , Regiones Promotoras GenéticasRESUMEN
Non-indigenous plants exhibit different attributes that make them aggressive competitors with indigenous plants and serious threats to biodiversity.Senecio madagascariensis (fireweed, Asteraceae), a native from southern Africa, is a strong competitor in agricultural activities and has toxic alkaloids that may result in high cattle mortality. In Brazil, this weed was collected for the first time in 1995 and has since spread quickly throughout the Pampas region. To better understand the invasion of the fireweed in South America, we used a genetic characterization with internal transcribed spacer (ITS) and microsatellite markers. Based on the ITS data, the southern Brazil populations of S. madagascariensis shared genetic homology with samples taken from the Hawaiian Islands and South Africa. Microsatellite analysis showed the genetic diversity split in two clusters, perhaps intimating the independent introduction of each species into South America. Although fireweed was introduced recently in southern Brazil, the considerable levels of genetic diversity, gene flow, and inbreeding may indicate success in the species establishment in this environment.
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DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using "best match" and "best close match" methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.
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ADN de Plantas/genética , ADN Espaciador Ribosómico/genética , Passiflora/genética , Código de Barras del ADN Taxonómico/métodos , Variación Genética/genética , Filogenia , Plastidios/genética , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Especificidad de la EspecieRESUMEN
The multigenic and multiallelic S-locus in plants is responsible for the gametophytic self-incompatibility system, which is important to prevent the detrimental effects of self-fertilization and inbreeding depression. Several studies have discussed the importance of punctual mutations, recombination, and natural selection in the generation of allelic diversity in the S-locus. However, there has been no wide-ranging study correlating the molecular evolution and structural aspects of the corresponding proteins in Solanum. Therefore, we evaluated the molecular evolution of one gene in this locus and generated a statistically well-supported phylogenetic tree, as well as evidence of positive selection, helping us to understand the diversification of S alleles in Solanum. The three-dimensional structures of some of the proteins corresponding to the major clusters of the phylogenetic tree were constructed and subsequently submitted to molecular dynamics to stabilize the folding and obtain the native structure. The positively selected amino acid residues were predominantly located in the hyper variable regions and on the surface of the protein, which appears to be fundamental for allele specificity. One of the positively selected residues was identified adjacent to a conserved strand that is crucial for enzymatic catalysis. Additionally, we have shown significant differences in the electrostatic potential among the predicted molecular surfaces in S-RNases. The structural results indicate that local changes in the three-dimensional structure are present in some regions of the molecule, although the general structure seems to be conserved. No previous study has described such structural variations in S-RNases.
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Ribonucleasas/genética , Solanum/genética , Alelos , Evolución Molecular , Variación Genética , Modelos Moleculares , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Ribonucleasas/química , Selección Genética , Alineación de Secuencia , Solanum/clasificación , Solanum/enzimologíaRESUMEN
The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome.
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Petunia/clasificación , Filogenia , Animales , Teorema de Bayes , ADN de Cloroplastos/genética , ADN de Plantas/genética , Evolución Molecular , Flores/anatomía & histología , Marcadores Genéticos , Funciones de Verosimilitud , Modelos Genéticos , Petunia/genética , Análisis de Secuencia de ADNRESUMEN
Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize.
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Núcleo Celular/genética , Petunia/genética , Filogenia , Plastidios/genética , Teorema de Bayes , Marcadores Genéticos , Variación Genética , Haplotipos , Hibridación Genética , Análisis de Secuencia de ADNRESUMEN
A total of 149 chickens from two different sources (one non-commercial, the other commercial) was tested for variability of the LEI0258 microsatellite. Fifty- three genotypes, explainable by 15 alleles, were found. There are clear allele and heterozygosity differences between the two samples. One of them was simultaneously studied for the MHC B-F haplotypes. Strong genetic disequilibrium was observed between the variants of the two systems, therefore providing a cheap alternative for MHC genotyping.
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Animales , Pollos/genética , Repeticiones de Microsatélite , Brasil , HaplotiposRESUMEN
Leaves from 14 Brazilian genotypes of Triticum aestivum L. were treated with salicylic acid to induce pathogenesis-related (PR) proteins. Inter and intracellular extracts were then obtained and investigated through polyacrilamide gel electrophoresis. Seven bands were observed. Material related to two of them (of 40 and 24 kDa) occurred in intracellular spaces only. DNA from these same genotypes was then amplified through PCR using primers developed from three sequences encoding PR proteins, and compared with previously described sequences. The fragments presented homologies to PR groups 1, 3 (chitinases), and 5 (thaumatin-like). The PR3-like sequence also showed a site characteristic of PRs induced by ethylene and a portion without homology with previous sequences. No variation among genotypes were observed, either for protein extracts or DNA sequences