Programa de Pós-Graduação em Botânica - PPGBot

LEM - Laboratório de Evolução Molecular

Departamento de Genética

Campus do Vale | Universidade Federal do Rio Grande do Sul | Porto Alegre, RS

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PUBLICAÇÕES

A lista a seguir representa algumas de nossas mais recentes publicações. Os links lhe darão acesso aos arquivos PDF se você tiver permissão das revistas. Alternativamente, busque no Portal de Periódicos CAPES ou entre em contato conosco.

Sistemática e Filogenia | Filogeografia e Estudos Populacionais | Evolução Molecular

Sistemática e Filogenia

Kulcheski, F; Muschner, VC; Lorenz-Lemke, AP; Stehmann, JR; Bonatto, SL; Salzano, FM; Freitas, LB (2006). Molecular phylogenetic analysis of Petunia Juss. (Solanaceae). Genetica,  126:3–14.

 Abstract - Representatives from 11 Petunia Jussieu species in south and southeast Brazil were compared with two Calibrachoa La Llave & Lex., one Bouchetia Dunal, and two Nierembergia Ruiz & Pav. taxa in relation to DNA molecular variability. A total of 4532 base pairs related to one nuclear, five plastidial and one mitochondrial systems was investigated. Petunia and Calibrachoa, although separated among themselves, clearly differentiate from the two other genera. Despite the fact that the Petunia species do not show marked molecular differences, they can be separated in two complexes, in good agreement with altitude data. Petunia + Calibrachoa should have diverged from other clades at about 25 million years before present.

Muschner,  VC; Lorenz-Lemke, AP; Vecchia, M; Bonatto, SL; Salzano, FM; Freitas, LB (2006). Differential organellar inheritance in Passiflora’s (Passifloraceae) subgenera. Genetica, 128:449-453.

 Abstract - Four chloroplast (cp), one mitochondrial (mt), and one ribosomal nuclear (ITS) DNA regions were studied in four artificial and one natural interspecific Passiflora hybrids. The ITS results confirmed their hybrid origin and all mtDNAs were maternally inherited. The same, however, was not true for cpDNA. The four hybrids (three artificial and one natural) derived from species of the Passiflora subgenus showed a cpDNA paternal inheritance, while the one involving taxa of the Decaloba subgenus gave evidence of maternal transmission. These results are of significance for the ongoing studies which are being performed on the molecular evolution of this genus and furnish important background for investigations aimed at clarifying the factors which determine cpDNA inheritance.

Muschner, VC; Lorenz, AP; Cervi, AC; Bonatto, SL; Souza-Chies, TT; Salzano, FM; Freitas, LB (2003). A first molecular phylogenetic analysis of Passiflora (Passifloraceae). American Journal of Botany, 90: 1229-1238.

Abstract  - Passiflora, a genus with more than 400 species, exhibits a high diversity of floral and vegetative structures and a complex taxonomy, which includes 23 subgenera and many sections and series. To better understand Passiflora’s variability and interspecific relationships, the phylogeny of 61 species, classified in 11 of 23 suggested subgenera, was investigated. Three molecular markers were used, the nuclear ribosomal internal transcribed spacers (nrITS), the plastid trnL-trnF spacer regions (;1000 bp), and the rps4 plastid gene (;570 bp). Three major clades were highly supported, independent of the marker and phylogenetic method used; one included the subgenera Distephana, Dysosmia, Dysosmioides, Passiflora, and Tacsonioides, a second, the subgenera Adopogyne, Decaloba, Murucuja, and Pseudomurucuja, and a third, the subgenus Astrophea. We call these the Passiflora, Decaloba, and Astrophea clades, respectively. The position of subgenus Deidamioides is undefined. The monophyly of Passiflora could not be statistically corroborated, and the relationships among the major clades and of these clades with the related genera remain unresolved. Our results indicate that a reevaluation of the monophyly of Passiflora and its infrageneric classification is necessary.

Filogeografia e Estudos Populacionais

Lorenz-Lemke, AP; Mäder, G; Muschner, VC; Stehmann, JR; Bonatto, SL; Salzano, FM; Freitas, LB (2006). Diversity and natural hybridization in a highly endemic species of Petunia (Solanaceae): a molecular and ecological analysis. Molecular Ecology, 15: 4487-4497.

 Abstract - Intrinsic reproductive barriers among the species of Petunia are weak and genetic isolation is obtained mainly by geographical separation and ecological diversification. The Serra do Sudeste region in the extreme south of Brazil is one of the centres of diversity of this genus and is characterized by the presence of species with different pollination syndromes. Petunia exserta is known only from four sandstone towers in a restricted area of this region (about 500 km²) and is characterized by its differentiated habitat (shelters in the sandstone towers) and by its floral characteristics adapted to ornithophily. In towers where this species is sympatric with the sphingophilous P. axillaris, phylogenetically close to P. exserta, we found plants with intermediate floral morphology, suggesting hybridization between them. To test this hypothesis and to better understand its consequences we analyzed the sequences of the plastid trnH-psbA, trnS-trnG and psbB-psbH intergenic spacers in 121 individuals sampled all over the P. exserta distribution. The joint analysis of the three markers revealed 13 haplotypes and the network showed two main genetic clades, which probably represent the original gene pool of the two species in the region. In general, individuals of a given population presented the same haplotype, independently of phenotype, corroborating the hybridization hypothesis. Field observations suggest that hummingbirds are responsible for the interspecific gene flow. Analysis of molecular variance revealed high inter-populational diversity among the towers. The low gene flow between populations is possibly related to the autochoric seed dispersion system.

Koehler-Santos, P; Lorenz-Lemke, AP; Muschner, VC; Bonatto, SL; Salzano, FM; Freitas, LB (2006).  Molecular genetic variation in Passiflora alata (Passifloraceae), an invasive species in southern Brazil. Biological Journal of Linneau Society 88: 611 - 630.

 Abstract  - A total of 85 wild plants were collected in different areas of southern and southeastern Brazil, and studied for nrDNA Internal Transcribed Spacers (ITS). Thirty-two of them were also investigated for two other nuclear (G3pdh and LEAFY), as well as eight plastid systems. Sixty-one ITS sequence types were identified, in a region of 412 base pairs (bp), while forty-two G3pdh haplotypes were found in a 1010 bp region, and 23 LEAFY haplotypes in a region of 565 bp. GC content was higher in ITS (65%) than in the two other nuclear regions (40%-42%), while nucleotide diversity was markedly higher in G3pdh than in the other two. But no variability was found in the plastid systems. Most of the nuclear molecular diversity (56%-86%) occurs at the intrapopulation level, there are clear evidences of population expansion, and little geographic structure in it. P. alata can therefore be characterized as a species that is actively colonizing previously unoccupied areas in southern Brazil. High indices of intrapopulation variability were found in the region that is being colonized, similar to those found in areas where P. alata is native. Multiple introductions, as well the species’ genetic structure and human interference may explain these findings.

Koehler-Santos, P; Lorenz-Lemke, AP; Salzano, FM; Freitas, LB (2006). Ecological-evolutionary relationships in Passiflora alata from Rio Grande do Sul, Brazil. Brazilian Journal of Biology 66 (3): 809-816.

 Abstract - The geographical distribution, ecological characteristics, flowering and fruiting times, and pollinating agents of Passiflora alata are considered and related to molecular genetic data gathered simultaneously. The first report on this species in Rio Grande do Sul was made in 1934, only in cultivated gardens. About 20 years latter, however, the species was already classified as efferata (wild) in Porto Alegre’s suburbs. The data presented here, together with the DNA investigations, indicate that P. alata is actively colonizing previously unoccupied areas of this region.

Lorenz-Lemke, AP; Muschner, VC; Bonatto, SL; Cervi, AC; Salzano, FM; Freitas, LB (2005). Phylogeographic inferences concerning evolution of Brazilian Passiflora actinia and P. elegans (Passifloraceae) based on ITS (nrDNA) variation. Annals of Botany 95: 799 –806.

Abstract  - Background and Aims Passiflora actinia and P. elegans, two markedly parapatric species, have their southern and northern distribution limits, respectively, in the most southern part of the Brazilian Atlantic Rain Forest. Despite the fact that they are classified in different taxonomic series, previous phylogenetic studies of this genus revealed a high genetic similarity between them. The aim of the present work was to analyse in more detail their geographical range in this region of overlap, to investigate intraspecific genetic variability and phylogeographic structure, and to search for possible hybrids. Methods Eighty-two localities were searched for these species, and nuclear internal transcribed spacer (ITS) sequences were investigated for 32 individuals of P. actinia, 20 of P. elegans and one putative interspecific hybrid. Plastid trnL-trnF and psbA-trnH were examined for 12 plants of each species and the putative hybrid. Key Results Both species showed a high level of intraspecific and intra-individual ITS variability. Network analysis revealed a north–south geographic gradient in their intra and interspecific relationships. Mismatch analyses suggested a recent population expansion of P. elegans. The plastid markers showed restricted variability but, together with the nuclear data, they contributed to the identification of an interspecific hybrid of intermediate morphology at the border of the distribution of these two species. Both genetic and morphological data indicate the absence of an extensive hybridization zone between these species. Conclusions Gene flow between lineages is the possible cause for the presence of different ITS sequences within a given plant, the absence of homogenization being due to the high degree of vegetative reproduction in the two species. Differentiation of P. actinia into geographic groups and the origin of P. elegans may have been influenced by the Atlantic Forest migration towards southern Brazil. The genetic pattern of the interspecific hybrid indicates that plastid inheritance in these species is at least sometimes paternal.

Evolução Molecular

Thompson^, CE; Salzano, FM; Souza, ON; Freitas^, LB. (2007) Sequence and structural aspects of the functional diversification of plant alcohol dehydrogenases. Gene (no prelo)

 Abstract - The glycolytic proteins in plants are coded by small multigene families, which provide an interesting contrast to the high copy number of gene families studied to date. The alcohol dehydrogenase (Adh) genes encode glycolytic enzymes that have been characterized in some plant families. Although the amino acid sequences of zinc-containing long-chain ADHs are highly conserved, the metabolic function of this enzyme is variable. They also have different patterns of expression and are submitted to differences in nonsynonymous substitution rates between gene copies. It is possible that the Adh copies have been retained as a consequence of adaptative amino acid replacements which have conferred subtle changes in function. Phylogenetic analysis indicates that there have been a number of separate duplication events within angiosperms, and that genes labeled Adh1, Adh2 and Adh3 in different groups may not be homologous. Nonsynonymous / synonymous ratios yielded no signs of positive selection. However, the coefficients of functional divergence (θ) estimated between the Adh1 and Adh2 gene groups indicate statistically significant site-specific shift of evolutionary rates between them, as well as between those of different botanical families, suggesting that altered functional constraints may have taken place at some amino acid residues after their diversification. The theoretical three-dimensional structure of the alcohol dehydrogenase from Arabis blepharophylla was constructed and verified to be stereochemically valid.

 Thompson, CE; Fernandes, CL; Souza, ON; Salzano, FM; Bonatto, SL; Freitas, LB (2006). Molecular Modelling of Pathogenesis-related Proteins of Family 5. Cell Biochemistry and Biophysics, 44: 385-394.

Abstract - The family of Pathogenesis-related (PR)-5 proteins have diverse functions, and some of them are classified as thaumatins, osmotins, inhibitors of a-amylase or trypsin. Although the specific function of many PR5 in plants is unknown, they are involved in the acquired systemic resistance and response to biotic stress, causing the inhibition of hyphal growth and reduction of spore germination probably by a membrane permeabilization mechanism or by interaction with pathogen receptors. We have constructed three-dimensional models of four proteins belonging to the Rosaceae and Fagaceae botanical families, using the technique of Comparative Molecular Modelling by Homology. There are four main structural differences between all the PR5, corresponding to regions with replacements of amino acids. Folding and the secondary structures are very similar for all of them. However, the isoelectric point and charge distributions differ for each protein.

Scherer, N; Thompson, CE; Freitas, LB; Bonatto, SL; Salzano, FM (2005). Patterns of molecular evolution in pathogenesis-related proteins. Genetics and Molecular Biology, 28: 645-653.

Abstract - The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 and 15 using an ML-based Bayesian method and likelihood ratio tests. These results confirm the importance of positive selection in proteins related to defense mechanisms already observed in a wide array of organisms.

Finkler, C; Giacomet, C; Muschner, VC; Salzano, FM; Freitas, LB (2005). Molecular investigations of pathogenesis-related Bet v 1 homologues in Passiflora (Passifloraceae). Genetica, 124: 117–125.

Abstract - The major birch pollen allergen, Bet v 1, responsible for allergic reactions in many areas of the world, is homologous to a large number of pathogenesis-related proteins (PRs), identified as PR10. As part of a long-range investigation of these types of proteins and of evolution in Passiflora, DNA sequences from eight Bet v 1 homologue isoforms were obtained from five species of this genus in Brazil, and their sequences compared among themselves and with 30 others from 8 different species, classified in different taxonomic units. The objective was a first characterization of these PRs in wild passionflowers, and their use for evolutionary and applied investigations. High interspecific, but low intraspecific variability was observed, as expected from multigenic families subjected to concerted evolution. The relationships obtained both within Passiflora and between it and seven other genera probably best reflect functional similarities than evolutionary history.

Freitas, LB; Bonatto, SL; Salzano, FM (2003). Evolutionary implications of intra- and interspecific molecular variability of pathogenesis-related proteins. Brazilian Journal of Biology, 63: 437-448.

 Abstract - We have examined phylogenetic relationships in seven pathogenesis-related (PR) protein families. Withinfamily comparisons involved 79 species, 166 amino acid sequences, and 1,791 sites. For 37 species, 124 different PR isoforms were identified (an average of 3.3 per species). Thirty-one of the 37 species investigated tended to cluster together (84%). Of the 17 clusters distinguished in the seven phylogenetic trees, 10 (59%) were in agreement with their taxonomic status, ascertained at the family level. The strong similarities among the intraspecific forms, as compared to interspecific differences, argue for some kind of gene conversion, but the rare occurrence of widely different isoforms also suggests diversifying selection. PRs 1, 6, and 4 seem to be less differentiated than PRs 3, 2, 10, and 5.

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