Papers by Carla De Freitas Munhoz
Semina-ciencias Agrarias, 2017
The genus Passiflora L. comprises around 500 species with different haploid numbers (n = 6, 9, 10... more The genus Passiflora L. comprises around 500 species with different haploid numbers (n = 6, 9, 10 e 12) and variability in the number of ribosomal DNA sites (rDNA). The subgenus Passiflora Juss. is one of the most diverse and includes several species of economic importance, such as Passiflora edulis and Passiflora alata Curtis, as well as Passiflora watsoniana Mast., which is endemic to Northeastern Brazil. These three species present 2n = 18 and two ( P. edulis , P. alata ) or three ( P. watsoniana ) pairs of 35S rDNA sites. In P. edulis, these sites are located in chromosomes 7 and 8, identified by fluorescent in situ hybridization (FISH) with chromosome-specific bacterial artificial chromosomes (BACs). With the aim of investigating the conservation of synteny between these species, we used FISH with BACs 173B16 and 164M13, markers for chromosome 7 and 8, respectively, followed by FISH with rDNA. As previously observed in P. edulis, 35S rDNA sites were observed in opposite arms to...
Chromosome Research, 2020
was originally published with incorrect values in Figure 4. The correct Figure 4 is presented below.
Chromosome Research, 2019
Passiflora edulis, the yellow passion fruit, is the main crop from the Passiflora genus, which co... more Passiflora edulis, the yellow passion fruit, is the main crop from the Passiflora genus, which comprises 525 species with its diversity center in South America. Genetic maps and a BAC (bacterial artificial chromosome) genomic library are available, but the nine chromosome pairs of similar size and morphology (2n = 18) hamper chromosome identification, leading to different proposed karyotypes. Thus, the aim of this study was to establish chromosome-specific markers for the yellow passion fruit using single-copy and repetitive sequences as probes in fluorescent in situ hybridizations (FISH) to allow chromosome identification and future integration with whole genome data. Thirty-six BAC clones harboring genes and three retrotransposons (Ty1-copy, Ty3-gypsy, and LINE) were selected. Twelve BACs exhibited a dispersed pattern similar to that revealed by retroelements, and one exhibited subtelomeric distribution. Twelve clones showed unique signals in terminal or subterminal regions of the chromosomes, allowing their genes to be anchored to six chromosome pairs that can be identified with single-copy markers. The markers developed herein will provide an important tool for genomic and evolutionary studies in the Passiflora genus.
Frontiers in Genetics, 2019
There is an error in the Funding statement. The correct number for Fundação de Amparo a Pesquisa ... more There is an error in the Funding statement. The correct number for Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP) is "2008/03969-4." The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.
Journal of the American Society for Horticultural Science, 2008
The development of genetic maps for auto-incompatible species, such as the yellow passion fruit (... more The development of genetic maps for auto-incompatible species, such as the yellow passion fruit (Passiflora edulis Sims f. flavicarpa Deg.) is restricted due to the unfeasibility of obtaining traditional mapping populations based on inbred lines. For this reason, yellow passion fruit linkage maps were generally constructed using a strategy known as two-way pseudo-testcross, based on monoparental dominant markers segregating in a 1:1 fashion. Due to the lack of information from these markers in one of the parents, two individual (parental) maps were obtained. However, integration of these maps is essential, and biparental markers can be used for such an operation. The objective of our study was to construct an integrated molecular map for a full-sib population of yellow passion fruit combining different loci configuration generated from amplified fragment length polymorphisms (AFLPs) and microsatellite markers and using a novel approach based on simultaneous maximum-likelihood estima...
Frontiers in genetics, 2018
Traditional sugarcane cultivars () proved highly susceptible to diseases, and this led breeders t... more Traditional sugarcane cultivars () proved highly susceptible to diseases, and this led breeders to progress to interspecific crosses resulting in disease resistance. A backcrossing program to was then required to boost sucrose content. Clonal selection across generations and incorporation of other germplasm into cultivated backgrounds established the (narrow) genetic base of modern cultivars ( spp.), which have a man-made genome. The genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture, and cytogenetics. However, there is a critical shortage of information on chromosome behavior throughout meiosis in modern cultivars. In this study, we examined the microsporogenesis of a contemporary variety, providing a detailed analysis of the meiotic process and chromosome association at diakinesis, using FISH with centromeric probes. Chromosomal abnormalities were documented by examining high quality preparations of ...
BMC Research Notes, 2017
Background: Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and un... more Background: Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). Results: A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. Conclusions: Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
Frontiers in plant science, 2017
The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all... more The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,72...
Phytopathology, Jan 9, 2015
The root-knot nematode (Meloidogyne incognita) is one of most devastating pathogens that attack t... more The root-knot nematode (Meloidogyne incognita) is one of most devastating pathogens that attack the common bean crop. Although there is evidence that some cultivars have race-specific resistance against M. incognita, these resistance sources have not proved effective, and nematodes are able to circumvent the host's defense system. We constructed RNA-seq based libraries and used a high-throughput sequencing platform to analyze the plant responses to M. incognita. Assessments were performed at 4 and 10 days after inoculation (DAI) corresponding to the stages of nematode penetration and giant cell development, respectively. Large-scale transcript mapping to the common bean reference genome (G19833) resulted in the identification of 27,195 unigenes. Of these, 797 host genes were found to be differentially expressed. The functional annotation results confirm the complex interplay between abiotic and biotic stress signaling pathways. High expression levels of the wounding responsive g...
Annals of Applied Biology, 2015
Passiflora edulis is the major species of passionflowers grown worldwide, mainly for juice produc... more Passiflora edulis is the major species of passionflowers grown worldwide, mainly for juice production and fresh fruit, in climates ranging from cool subtropical (purple variety) to warm tropical (yellow variety). The bacterial leaf spot, caused by Xanthomonas axonopodis pv. passiflorae (Xap) can be a serious disease affecting passion fruit production in commercial orchards, particularly under moist field conditions. In this study we describe a first analysis of host gene expression in this pathosystem. We used suppression subtractive hybridization to construct two cDNA libraries enriched for transcripts induced and repressed by Xap, respectively, 24 h post inoculation with a highly virulent strain. High-quality sequences were obtained resulting in 998 unisequences that were used for annotation. In accordance with BLASTX results performed by Blast2GO tool, 86.7% of the unisequences showed similarity to other plant species' proteins related to different functional categories. Sixty-three transcripts were similar to Arabidopsis thaliana defence-related proteins identified in the PLAZA platform. In silico predicted protein-protein interactions were detected on the basis of the STRING database for 35 of the 63 defence-related proteins. At this early stage of interaction, a set of genes was selected from Blast2GO categorization results and analysed by quantitative PCR (qPCR). The expression profiles changed in response to the pathogen for 76% of these genes (48/63) and the differences in expression ratios ranged from 0.51-fold to 1.83-fold. In later stages of interactions (5 and 9 days post inoculation) when disease-associated symptoms were visible, qPCR analyses were performed for 14 genes selected from both libraries. The expression profiles of all genes were found to be changed by the pathogen. The gene that responded most strongly to the pathogen attack encodes a lipoxygenase 2. In inoculated plants, its expression was induced 500-fold and 300-fold, 5 and 9 dpi, respectively, compared to controls, suggesting an important role of this gene in passion fruit defence. Moreover, we showed that most of the genes involved in well-known pathogen recognition signalling pathways were repressed by Xap and this lends support to the idea that the jasmonic acid signalling pathway fails to be activated during the first hours of interaction.
International Journal of Food Microbiology, 2014
The exploitation of the Brazil nut is one of the most important activities of the extractive comm... more The exploitation of the Brazil nut is one of the most important activities of the extractive communities of the Amazon rainforest. However, its commercialization can be affected by the presence of aflatoxins produced by fungi, namely Aspergillus section Flavi. In the present study, we investigated a collection of Aspergillus nomius strains isolated from Brazil nuts using different approaches, including morphological characters, RAPD and AFLP profiles, partial β-tubulin and calmodulin nucleotide sequences, aflatoxin patterns, as well as tolerance to low water activity in cultured media. Results showed that most of the isolates do belong to A. nomius species, but a few were re-identified as Aspergillus pseudonomius, a very recently described species. The results of the analyses of molecular variance, as well as the high pairwise F ST values between A. nomius and A. pseudonomius suggested the isolation between these two species and the inexistence of gene flow. Fixed interspecific nucleotide polymorphisms at β-tubulin and calmodulin loci are presented. All A. pseudonomius strains analyzed produced aflatoxins AFB1, AFB2, AFG1 and AFG2. This study contains the first-ever report on the occurrence in Brazil nuts of A. pseudonomius. The G-type aflatoxins and the mycotoxin tenuazonic acid are reported here for the first time in A. pseudonomius.
Phytopathology®, 2011
Xanthomonas axonopodis pv. passiflorae causes bacterial spot in passion fruit. It attacks the pur... more Xanthomonas axonopodis pv. passiflorae causes bacterial spot in passion fruit. It attacks the purple and yellow passion fruit as well as the sweet passion fruit. The diversity of 87 isolates of pv. passiflorae collected from across 22 fruit orchards in Brazil was evaluated using molecular profiles and statistical procedures, including an unweighted pair-group method with arithmetical averages-based dendrogram, analysis of molecular variance (AMOVA), and an assigning test that provides information on genetic structure at the population level. Isolates from another eight pathovars were included in the molecular analyses and all were shown to have a distinct repetitive sequence-based polymerase chain reaction profile. Amplified fragment length polymorphism technique revealed considerable diversity among isolates of pv. passiflorae, and AMOVA showed that most of the variance (49.4%) was due to differences between localities. Cluster analysis revealed that most genotypic clusters were ho...
Indian Journal of Microbiology, 2012
The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana c... more The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88 % of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5 0-TGC GGC TGA GGA GGA CT-3 0) and BbasCG1024R (5 0-TGC GGC TGA GTG TAG AAC-3 0) were designed for detecting and monitoring this isolate in the field.
Annals of Applied Biology, 2013
ABSTRACT One of the current challenges of tropical fruit crop improvement is to incorporate molec... more ABSTRACT One of the current challenges of tropical fruit crop improvement is to incorporate molecular marker-based approaches into conventional breeding programmes. This study was designed to build an integrated genetic map of the sweet passion fruit (Passiflora alata), a diploid (2n=18) outcrossing species which is greatly appreciated for in natura consumption, and reported to inspire cosmetic and pharmaceutical companies to create plant-derived compounds. With this in mind, a full-sib family of 180 individuals was genotyped using different molecular marker types, such as amplified fragment length polymorphisms (AFLP), microsatellite-AFLP (M-AFLP), simple sequence repeats (SSR), resistance gene analogues (RGA) and target region amplification polymorphism (TRAP). On average, the rate of polymorphism between the parental genotypes was 20.3%. We also searched for single nucleotide polymorphisms (SNPs) in some AFLP bands and in seven gene fragments, and found one SNP every 87bp. All SNPs were biallelic and occurred most frequently in putative gene fragments (81.5%) rather than in AFLP bands (60.0%) analyzed. Excellent gel profiles were obtained allowing the recognition of all types of segregation expected for a progeny of an outcrossing species. Multipoint linkage analysis was performed using OneMap software, with logarithm of the odds (LOD) score5.6 and recombination fraction <0.5. The resulting integrated map consists of 549 markers, 2.0% of which fit a segregation ratio of 1:1:1:1, 1.3% a ratio of 1:2:1, 27.3% a ratio of 3:1 and 69.4% a ratio of 1:1. The map spanned a total of 2073.0cM, with an average distance between adjacent markers of 3.8cM. This is the first linkage study on sweet passion fruit and should prove useful for quantitative trait loci mapping.
BMC Genomics, 2014
Background: The passion fruit (Passiflora edulis) is a tropical crop of economic importance both ... more Background: The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a prerequisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. Results: The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). Conclusions: We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified.
Scientific Reports, 2018
Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for ind... more Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes. The Passifloraceae family belongs to the Malpighiales order and is a member of the Rosids clade, according to classical and molecular phylogenetic analysis. The family consists of 700 species, classified in 16 genera. The majority of species belong to the genus Passiflora (~530 species), popularly known as passion fruits 1. This genus is widely distributed in tropical and subtropical regions of the Neotropics. Approximately 150 species are native to Brazil, which is acknowledged to be an important centre of diversity 2. Among the American tropical species of Passiflora, 60 fruit-bearing species are marketed for human consumption. Moreover, several species and hybrids have been produced for ornamental purposes (see www.passiflora.it;) 3 , and pharmacologists have found that passion fruit vines contain bioactive compounds that are used in traditional folk medicines as anxiolytics and antispasmodics 4. Passiflora edulis is the major species of passionflowers grown for fresh fruit consumption and juice production in climates ranging from cool subtropical (purple variety) to warm tropical (yellow variety). Species grown particularly in Brazil include P. edulis (sour passion fruit) and P. alata (sweet passion fruit). Because of the quality of its fruit and yield for processing into commercial
Genetics and Molecular Biology, 2016
Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics stud... more Microsatellites or Single Sequence Repeats (SSRs) are extensively employed in plant genetics studies, using both low and high throughput genotyping approaches. Motivated by the importance of these sequences over the last decades this review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function. The methodologies for the development of SSR loci, genotyping and their applications as molecular markers are also reviewed. Finally, two data surveys are presented. The first was conducted using the main database of Web of Science, prospecting for articles published over the period from 2010 to 2015, resulting in approximately 930 records. The second survey was focused on papers that aimed at SSR marker development, published in the American Journal of Botany's Primer Notes and Protocols in Plant Sciences (over 2013 up to 2015), resulting in a total of 87 publications. This scenario confirms the current relevance of SSRs and indicates their continuous utilization in plant science.
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Papers by Carla De Freitas Munhoz