In silico comparative analysis of tylenchid nematode pectate lyases.

Phytoparasitic nematodes can infect a wide range of crop plants, and cause billions of dollars of agricultural losses each year. These parasites represent the largest source of biotic stress experienced by plants. The order Tylenchida comprises the most important parasitic nematodes, particularly the root-knot and cyst nematodes. These parasitic organisms obtain nutrients to support their development through complex interactions with their hosts. Plant-parasitic nematodes secrete a mixture of cell-wall degrading enzymes to facilitate migration through the plant root. Enzymes are secreted that degrade the principal cell-wall components, cellulose, hemi-cellulose, or pectin. Pectate lyases are important parasitism factors in plant-parasitic nematodes. These enzymes degrade polygalacturonic acid, which is a fundamental constituent of pectin of host cell walls. Thus, pectate lyases permit the penetration and colonization of plant host cells by parasites. Here, we analyzed 22 pectate lyase protein sequences from tylenchid nematode species. Our results revealed great variation in the isoelectric points of pectate lyases, and groups of acidic and alkaline proteins that may have distinct enzymatic activities were identified. Phylogenetic analysis also revealed the presence of two main groups of pectate lyases with distinct chemical properties. Seven conserved motifs were identified, but only five were present in all sequences. Results of the molecular docking analysis revealed differences in the predicted interaction sites in the pectate lyases from the two groups. These results may provide a theoretical basis for future studies of host plant resistance to nematode infection.

Genetic diversity and morphological characterization of half-sib families of Heliconia bihai L., H. chartacea Lane ex Barreiros, and H. wagneriana Peterson.

The Neotropical Heliconia genus contains highly diversified plants and up to 220 species have been reported from the north of Mexico to the South of Brazil. Heliconia are cultivated as ornamental garden plants and as cut flowers. All species can be propagated by seeds or vegetatively, through rhizomes. Depending on the species, an individual plant can spread and form large clonal populations. H. bihai L., H. chartacea Lane ex Barreiros, and H. wagneriana Petersen are among the most cultivated Heliconia species. However, they still have undesirable characteristics that could be improved for the international market. This study aimed to characterize 15 half-sib families originating from commercial cultivations, by morphological and molecular markers. The genetic diversity (HE), considering all individuals of the three species was 0.103. For H. bihai half-sib families, the value of HE was 0.242, showing high genetic diversity. The HE value for H. chartacea was 0.068, indicating low genetic diversity. All individuals of H. wagneriana showed the same band patterns, suggesting that the two parental plants were propagated vegetatively from the same plant and may have undergone some endogamic crossings. These results showed that molecular characterization can differentiate individuals closely related as half-siblings for H. bihai and H. chartacea, despite the low variation observed with morphological descriptors. The high genetic diversity observed in H. bihai half-sibling genotypes can provide valuable resources for breeding programs.

Fragmentation effects and genetic diversity of the key semidecidual forest species Metrodorea nigra in Southwestern Brazil.

Studies of genetic diversity in plant species present in the remaining fragments of the Atlantic Forest are very important for understanding their resilience to such a degraded ecosystem. We analyzed the genetic diversity of 3 populations of the high-density understory species Metrodorea nigra St. Hill. (Rutaceae) located in forest remnants in the region of Ribeirão Preto, SP, Brazil (M13-Rib, BSQ-Rib, and FAC-Crav), by using simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) molecular markers for conservation purposes. A total of 133 polymorphic loci were observed in 136 inter-simple sequence repeat loci (average of 17 per primer). The Nei genetic diversity (HE) was relatively high considering all populations (0.31). The BSQ-Rib population exhibited the highest value (0.27), followed by the M13-Rib (0.26) and FAC-Crav (0.24) populations. The simple sequence repeat markers analyzed showed a high number of alleles (K = 104), with an average of 14.85 alleles per locus. The average observed heterozygosity was 0.516 and the average expected heterozygosity was 0.771, ranging from 0.688 (FAC-Crav) to 0.765 (BSQ-Rib). The fixation indexes showed positive and significant differences from zero for all sample sets, indicating inbreeding, which may have resulted from the species' mating patterns and the barochoric seed dispersal system of M. nigra. Both markers indicated differentiation among populations, with higher values observed for inter-simple sequence repeat markers. No significant differences between juvenile and adult generations in any of the fragments were observed, indicating the resilience of M. nigra to the effects of fragmentation and reduced habitat.

Genetic diversity of the Neotropical tree Hancornia speciosa Gomes in natural populations in Northeastern Brazil.

Mangabeira (Hancornia speciosa Gomes) is a fruit tree of the Apocynaceae family, which is native to Brazil and is a very important food resource for human populations in its areas of occurrence. Mangabeira fruit is collected as an extractive activity, and no domesticated varieties or breeding programs exist. Due to a reduction in the area of ecosystems where it occurs, mangabeira is threatened by genetic erosion in Brazil. The objective of this study was to characterize and evaluate the genetic diversity of 38 mangabeira individuals collected from natural populations in Pernambuco State using inter-simple sequence repeat (ISSR) molecular markers. The ISSR methodology generated a total of 93 loci; 10 were monomorphic and 83 were polymorphic. The average number of loci per primer was 15.5, ranging from 9 (#UBC 866) to 21 (#UBC 834). The results showed a high level of genetic diversity (0.30), and found that only around 30% of genetic variability is distributed among populations (GST = 0.29, ФST = 0.30), with the remainder (ФCT = 70%) found within each population, as expected for forest outcrossing species. Estimates for historic gene flow (1.18) indicate that there is some isolation of these populations, and some degree of genetic differentiation.

Genetic variability in accessions of the acerola germplasm bank of Universidade Federal Rural de Pernambuco, Brazil.

Brazil is the world's largest producer of acerola, Malpighia emarginata (Malpighiaceae); the Northeast is responsible for 60% of the national production. The culture of acerola in Brazil has great genetic variability; plantings have high phenotypic diversity and are not very productive, often originating from propagation by seed. We evaluated the genetic diversity of 42 accessions from the Acerola Active Germplasm Bank of Universidade Federal de Pernambuco. Using 15 RAPD primers, 182 markers were obtained, of which 166 were polymorphic and 16 were monomorphic. We found high genetic variability among the accessions (HE = 0.29), with no redundancy. Considering the accessions from the states of Pernambuco, Bahia and Pará as distinct groups, there was greater diversity in accessions from Bahia than from the other two states.