Publications by authors named "Ana Maria Benko-Iseppon"

54 Publications

Plant Antimicrobial Peptides as Potential Tool for Topic Treatment of Hidradenitis Suppurativa.

Front Microbiol 2021 13;12:795217. Epub 2021 Dec 13.

Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar.

Among chronic skin autoinflammatory diseases, Hidradenitis Suppurativa (HS) stands out for its chronicity, highly variable condition, and profound impact on the patients' quality of life. HS is characterized by suppurative skin lesions in diverse body areas, including deep-seated painful nodules, abscesses, draining sinus, and bridged scars, among others, with typical topography. To date, HS is considered a refractory disease and medical treatments aim to reduce the incidence, the infection, and the pain of the lesions. For this purpose, different classes of drugs, including anti-inflammatory molecules, antibiotics and biological drugs are being used. Antimicrobial peptides (AMPs), also called defense peptides, emerge as a new class of therapeutic compounds, with broad-spectrum antimicrobial action, in addition to reports on their anti-inflammatory, healing, and immunomodulating activity. Such peptides are present in prokaryotes and eukaryotes, as part of the innate eukaryotic immune system. It has been proposed that a deregulation in the expression of AMPs in human epithelial tissues of HS patients may be associated with the etiology of this skin disease. In this scenario, plant AMPs stand out for their richness, diversity of types, and broad antimicrobial effects, with potential application for topical systemic use in patients affected by HS.
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http://dx.doi.org/10.3389/fmicb.2021.795217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8710806PMC
December 2021

Antioxidant and cytogenotoxic properties of (Allemão) A.C.Sm. leaf extract.

Drug Chem Toxicol 2021 Dec 14:1-9. Epub 2021 Dec 14.

Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.

leaves have been used in folk medicine to treat respiratory diseases and inflammations. This study aimed to evaluate the biological potential of leaves by antioxidant and cytogenotoxic analyses of ethanolic crude extract (EE) and its fractions in healthy human cells. The EE was obtained by percolation, followed by fractionation using dichloromethane, cyclohexane, ethyl acetate (EtOAc), and methanol (MeOH) as organic solvents. Extract and all fractions were evaluated for their antioxidant potential by DPPH and reducing power tests. cytotoxic activity was determined in human peripheral blood mononuclear cells by MTT assay for the extract, EtOAc and MeOH fractions. In turn, the genotoxic activity was determined in human lymphocytes by the Cytokinesis Block Micronucleus assay only for the EtOAc fraction. Only EtOAc fraction was analyzed via gas chromatography coupled to mass spectrometry due to its higher biological activity. Considering the antioxidant potential, the EtOAc fraction was most effective in DPPH (EC 43.37 µg/mL) and reducing power (EC 89.80 µg/mL) assays. GC-MS analysis of the EtOAc fraction led to the identification of guaiacol, 2,3-dihydro-benzofuran, 2-methoxy-4-vinylphenol, isovanillic acid methyl ester, 4-hydroxybenzaldehyde, and 4-(ethoxymethyl)-phenol. The EE (400-1000 µg/mL), EtOAc (≤150 µg/mL) and MeOH (50 and 150-600 µg/mL) fractions were not cytotoxic by MTT test. Additionally, the EtOAc fraction (100-400 µg/mL) did not induce significant genotoxic damage. Concentrations of the EtOAc fraction with antioxidant activity showed no cytotoxicity, nor genotoxicity potential, indicating them as a nontoxic natural antioxidant source.
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http://dx.doi.org/10.1080/01480545.2021.2011313DOI Listing
December 2021

Lipid Transfer Proteins (LTPs)-Structure, Diversity and Roles beyond Antimicrobial Activity.

Antibiotics (Basel) 2021 Oct 21;10(11). Epub 2021 Oct 21.

Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil.

Lipid transfer proteins (LTPs) are among the most promising plant-exclusive antimicrobial peptides (AMPs). They figure among the most challenging AMPs from the point of view of their structural diversity, functions and biotechnological applications. This review presents a current picture of the LTP research, addressing not only their structural, evolutionary and further predicted functional aspects. Traditionally, LTPs have been identified by their direct isolation by biochemical techniques, whereas omics data and bioinformatics deserve special attention for their potential to bring new insights. In this context, new possible functions have been identified revealing that LTPs are actually multipurpose, with many additional predicted roles. Despite some challenges due to the toxicity and allergenicity of LTPs, a systematic review and search in patent databases, indicate promising perspectives for the biotechnological use of LTPs in human health and also plant defense.
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http://dx.doi.org/10.3390/antibiotics10111281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8615156PMC
October 2021

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.

World J Microbiol Biotechnol 2021 Oct 28;37(12):206. Epub 2021 Oct 28.

Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
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http://dx.doi.org/10.1007/s11274-021-03168-2DOI Listing
October 2021

Oligo-FISH barcode in beans: a new chromosome identification system.

Theor Appl Genet 2021 Nov 8;134(11):3675-3686. Epub 2021 Aug 8.

Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil.

Key Message: An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7-15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.
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http://dx.doi.org/10.1007/s00122-021-03921-zDOI Listing
November 2021

The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses.

Front Plant Sci 2021 14;12:667013. Epub 2021 Jun 14.

Laboratory of Plant Genetics and Biotechnology, Genetics Department, Federal University of Pernambuco, Recife, Brazil.

The present work represents a pioneering effort, being the first to analyze genomic and transcriptomic data from (cowpea) kinases. We evaluated the cowpea kinome considering its genome-wide distribution and structural characteristics (at the gene and protein levels), sequence evolution, conservation among Viridiplantae species, and gene expression in three cowpea genotypes under different stress situations, including biotic (injury followed by virus inoculation-CABMV or CPSMV) and abiotic (root dehydration). The structural features of cowpea kinases (VuPKs) indicated that 1,293 VuPKs covered 20 groups and 118 different families. The RLK-Pelle was the largest group, with 908 members. Insights on the mechanisms of VuPK genomic expansion and conservation among Viridiplantae species indicated dispersed and tandem duplications as major forces for VuPKs' distribution pattern and high orthology indexes and synteny with other legume species, respectively. / ratios showed that almost all (91%) of the tandem duplication events were under purifying selection. Candidate -regulatory elements were associated with different transcription factors (TFs) in the promoter regions of the RLK-Pelle group. C2H2 TFs were closely associated with the promoter regions of almost all scrutinized families for the mentioned group. At the transcriptional level, it was suggested that VuPK up-regulation was stress, genotype, or tissue dependent (or a combination of them). The most prominent families in responding (up-regulation) to all the analyzed stresses were RLK-Pelle_DLSV and CAMK_CAMKL-CHK1. Concerning root dehydration, it was suggested that the up-regulated VuPKs are associated with ABA hormone signaling, auxin hormone transport, and potassium ion metabolism. Additionally, up-regulated VuPKs under root dehydration potentially assist in a critical physiological strategy of the studied cowpea genotype in this assay, with activation of defense mechanisms against biotic stress while responding to root dehydration. This study provides the foundation for further studies on the evolution and molecular function of VuPKs.
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http://dx.doi.org/10.3389/fpls.2021.667013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238008PMC
June 2021

Reference genes for quantitative real-time PCR normalization of Cenostigma pyramidale roots under salt stress and mycorrhizal association.

Genet Mol Biol 2021 31;44(2):e20200424. Epub 2021 May 31.

Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.

Cenostigma pyramidale is a native legume of the Brazilian semiarid region which performs symbiotic association with arbuscular mycorrhizal fungi (AMF), being an excellent model for studying genes associated with tolerance against abiotic and biotic stresses. In RT-qPCR approach, the use of reference genes is mandatory to avoid incorrect interpretation of the relative expression. This study evaluated the stability of ten candidate reference genes (CRGs) from C. pyramidale root tissues under salt stress (three collection times) and associated with AMF (three different times of salinity). The de novo transcriptome was obtained via RNA-Seq sequencing. Three algorithms were used to calculate the stability of CRGs under different conditions: (i) global (Salt, Salt+AMF, AMF and Control, and collection times), (ii) only non-inoculated plants, and (iii) AMF (only inoculated plants). HAG2, SAC1, aRP3 were the most stable CRGs for global and AMF assays, whereas HAG2, SAC1, RHS1 were the best for salt stress assay. This CRGs were used to validate the relative expression of two up-regulated transcripts in Salt2h (RAP2-3 and PIN8). Our study provides the first set of reference genes for C. pyramidale under salinity and AMF, supporting future researches on gene expression with this species.
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http://dx.doi.org/10.1590/1678-4685-GMB-2020-0424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167929PMC
May 2021

Transcriptome of Cenostigma pyramidale roots, a woody legume, under different salt stress times.

Physiol Plant 2021 Dec 24;173(4):1463-1480. Epub 2021 May 24.

Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.

Salinity stress has a significant impact on the gain of plant biomass. Our study provides the first root transcriptome of Cenostigma pyramidale, a tolerant woody legume from a tropical dry forest, under three different salt stress times (30 min, 2 h, and 11 days). The transcriptome was assembled using the RNA sequencing (RNA-Seq) de novo pipeline from GenPipes. We observed 932, 804, and 3157 upregulated differentially expressed genes (DEGs) and 164, 273, and 1332 downregulated DEGs for salt over 30 min, 2 h, and 11 days, respectively. For DEGs annotated with the Viridiplantae clade in the early stress periods, the response to salt stress was mainly achieved by stabilizing homeostasis of such ions like Na and K , signaling by Ca , transcription factor modulation, water transport, and oxidative stress. For salt stress at 11 days, we observed a higher modulation of transcription factors including the WRKY, MYB, bHLH, NAC, HSF, and AP2-EREBP families, as well as DEGs involved in hormonal responses, water transport, sugar metabolism, proline, and reactive oxygen scavenging mechanisms. Five selected DEGs (K transporter, aquaporin, glutathione S-transferase, cyclic nucleotide-gated channel, and superoxide dismutase) were validated by qPCR. Our results indicated that C. pyramidale had an early perception of salt stress modulating ionic channels and transporters, and as the stress progressed, the focus turned to the antioxidant system, aquaporins, and complex hormone responses. The results of this first root transcriptome provide clues on how this native species modulate gene expression to achieve salt stress tolerance.
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http://dx.doi.org/10.1111/ppl.13456DOI Listing
December 2021

Evaluation of quality and gene expression of goat embryos produced in vivo and in vitro after cryopreservation.

Cryobiology 2021 08 5;101:115-124. Epub 2021 May 5.

Laboratory of Reproductive Biotechniques, Department of Veterinary Medicine, Federal Rural University of Pernambuco, Brazil. Electronic address:

In the present study, we aimed to identify morphological and molecular changes of in vivo and in vitro-produced goat embryos submitted to cryopreservation. In vivo embryos were recovered by transcervical technique from superovulated goats, whereas in vitro produced embryos were produced from ovaries collected at a slaughterhouse. Embryos were frozen by two-steps slow freezing method, which is defined as freezing to -32 °C followed by transfer to liquid nitrogen. Morphological evaluation of embryos was carried out by assessing blastocoel re-expansion rate and the total number of blastomeres. The expression profile of candidate genes related to thermal and oxidative stress, apoptosis, epigenetic, and implantation control was measured using RT-qPCR based SYBR Green system. In silico analyses were performed to identify conserved genes in goat species and protein-protein interaction networks were created. In vivo-produced embryos showed greater blastocoel re-expansion and more blastomere cells (P < 0.05). The expression level of CTP2 and HSP90 genes from in vitro cryopreserved embryos was higher than their in vivo counterparts. Unlikely, no significant difference was observed in the transcription level of SOD gene between groups. The high similarity of CPT2 and HSP90 proteins to their orthologs among mammals indicates that they share conserved functions. In summary, cryopreservation negatively affects the morphology and viability of goat embryos produced in vitro and changes the CPT2 and HSP90 gene expression likely in response to the in vitro production process.
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http://dx.doi.org/10.1016/j.cryobiol.2021.04.008DOI Listing
August 2021

BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris.

Chromosoma 2021 09 28;130(2-3):133-147. Epub 2021 Apr 28.

Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil.

Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.
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http://dx.doi.org/10.1007/s00412-021-00758-9DOI Listing
September 2021

Salt tolerance of begins with immediate regulation of aquaporin activity in the root system.

Physiol Mol Biol Plants 2021 Mar 20;27(3):457-468. Epub 2021 Feb 20.

Laboratório de Fisiologia Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE 50670-901 Brazil.

The ability to respond quickly to salt stress can determine the tolerance level of a species. Here, we test how rapidly the roots of react to high salinity conditions. In the first 24 h after saline exposure, the plants reduced stomatal conductance, increased CO assimilation, and water use efficiency. Thus, the root tissue showed an immediate increase in soluble sugars, free amino acid, and soluble protein contents. Twelve aquaporins showed differential gene expression in the roots of under salinity. Transcriptional upregulation was observed only after 2 h, with greater induction of (fourfold). Transcriptional downregulation, in turn, occurred mainly after 8 h, with the largest associated with (fourfold). plants responded quickly to high saline levels. Our results showed a strong stomatal control associated with high free amino acid and soluble sugar contents, regulated aquaporin expression in roots, and supported the high performance of the root system of under salinity. Moreover, this species was able to maintain a lower Na/K ratio in the leaves compared to that of the roots of stressed plants. The first response of the root system, after immediate contact with saline solution, present an interesting scenario to discuss.

Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-021-00957-9.
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http://dx.doi.org/10.1007/s12298-021-00957-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7981346PMC
March 2021

Cassava (Manihot esculenta) defensins: Prospection, structural analysis and tissue-specific expression under biotic/abiotic stresses.

Biochimie 2021 Jul 28;186:1-12. Epub 2021 Mar 28.

Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil. Electronic address:

Defensins are a prominent family of antimicrobial peptides. They play sophisticated roles in the defense against pathogens in all living organisms, but few works address their expression under different conditions and plant tissues. The present work prospected defensins of Manihot esculenta Crantz, popularly known as cassava. Five defensin candidates (MeDefs) were retrieved from the genome sequences and characterized. Considering chromosome distribution, only MeDef1 and 2 occupy adjacent positions in the same chromosome arm. All 3D structures had antiparallel ß-sheets, an α-helix, and amphipathic residues distributed throughout the peptides with a predominance of cationic surface charge. MeDefs expression was validated by RT-qPCR, including two stress types (biotic: fungus Macrophomina pseudophaseolina, and abiotic: mechanical injury) and a combination of both stresses (fungus+injury) in three different tissues (root, stem, and leaf). For this purpose, ten reference genes (RGs) were tested, and three were chosen to characterize MeDef expression. MeDef3 was up-regulated at roots in all stress situations tested. MeDef1 and MeDef5 were induced in leaves under biotic and abiotic stresses, but not in both stress types simultaneously. Only MeDef2 was down-regulated in the stem tissue also with biotic/abiotic combined stresses. These results indicate that although defensins are known to be responsive to pathogen infection, they may act as preformed defense or, still, have tissue or stress specificities. Aspects of their structure, stability and evolution are also discussed.
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http://dx.doi.org/10.1016/j.biochi.2021.03.012DOI Listing
July 2021

Antimicrobial peptides in the seedling transcriptome of the tree legume Peltophorum dubium.

Biochimie 2021 Jan 13;180:229-242. Epub 2020 Nov 13.

Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay; Instituto de Química Biológica, Facultad de Ciencias - Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11800, Uruguay. Electronic address:

Antimicrobial peptides (AMPs) play an essential role in plant defense against invading pathogens. Due to their biological properties, these molecules have been considered useful for drug development, as novel agents in disease therapeutics, applicable to both agriculture and medicine. New technologies of massive sequencing open opportunities to discover novel AMP encoding genes in wild plant species. This work aimed to identify cysteine-rich AMPs from Peltophorum dubium, a legume tree from South America. We performed whole-transcriptome sequencing of P. dubium seedlings followed by de novo transcriptome assembly, uncovering 78 AMP transcripts classified into five families: hevein-like, lipid-transfer proteins (LTPs), alpha hairpinins, defensins, and snakin/GASA (Giberellic Acid Stimulated in Arabidopsis) peptides. No transcripts with similarity to cyclotide or thionin genes were identified. Genomic DNA analysis by PCR confirmed the presence of 18 genes encoding six putative defensins and 12 snakin/GASA peptides and allowed the characterization of their exon-intron structure. The present work demonstrates that AMP prediction from a wild species is possible using RNA sequencing and de novo transcriptome assembly, regarding a starting point for studies focused on AMP gene evolution and expression. Moreover, this study allowed the detection of strong AMP candidates for drug development and novel biotechnological products.
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http://dx.doi.org/10.1016/j.biochi.2020.11.005DOI Listing
January 2021

Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era.

Bioinform Biol Insights 2020 2;14:1177932220952739. Epub 2020 Sep 2.

Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.

Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.
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http://dx.doi.org/10.1177/1177932220952739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476358PMC
September 2020

LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks.

BMC Bioinformatics 2020 Aug 24;21(1):365. Epub 2020 Aug 24.

University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, Esch-sur-Alzette, Luxembourg.

Background: The amount of published full-text articles has increased dramatically. Text mining tools configure an essential approach to building biological networks, updating databases and providing annotation for new pathways. PESCADOR is an online web server based on LAITOR and NLProt text mining tools, which retrieves protein-protein co-occurrences in a tabular-based format, adding a network schema. Here we present an HPC-oriented version of PESCADOR's native text mining tool, renamed to LAITOR4HPC, aiming to access an unlimited abstract amount in a short time to enrich available networks, build new ones and possibly highlight whether fields of research have been exhaustively studied.

Results: By taking advantage of parallel computing HPC infrastructure, the full collection of MEDLINE abstracts available until June 2017 was analyzed in a shorter period (6 days) when compared to the original online implementation (with an estimated 2 years to run the same data). Additionally, three case studies were presented to illustrate LAITOR4HPC usage possibilities. The first case study targeted soybean and was used to retrieve an overview of published co-occurrences in a single organism, retrieving 15,788 proteins in 7894 co-occurrences. In the second case study, a target gene family was searched in many organisms, by analyzing 15 species under biotic stress. Most co-occurrences regarded Arabidopsis thaliana and Zea mays. The third case study concerned the construction and enrichment of an available pathway. Choosing A. thaliana for further analysis, the defensin pathway was enriched, showing additional signaling and regulation molecules, and how they respond to each other in the modulation of this complex plant defense response.

Conclusions: LAITOR4HPC can be used for an efficient text mining based construction of biological networks derived from big data sources, such as MEDLINE abstracts. Time consumption and data input limitations will depend on the available resources at the HPC facility. LAITOR4HPC enables enough flexibility for different approaches and data amounts targeted to an organism, a subject, or a specific pathway. Additionally, it can deliver comprehensive results where interactions are classified into four types, according to their reliability.
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http://dx.doi.org/10.1186/s12859-020-03620-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7447576PMC
August 2020

Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population.

J Clin Pathol 2021 Aug 5;74(8):528-532. Epub 2020 Aug 5.

Department of Advanced Diagnostics, IRCCS Materno Infantile Burlo Garofolo, Trieste, Friuli Venezia Giulia, Italy.

Aims: Brazil is nowadays one of the epicentres of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and new therapies are needed to face it. In the context of specific immune response against the virus, a correlation between Major Histocompatibility Complex Class I (MHC-I) and the severity of the disease in patients with COVID-19 has been suggested. Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods.

Methods: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes.

Results: We identified 24 immunogenic epitopes in the SARS-CoV-2 protein S that could interact with 17 different MHC-I alleles (namely, HLA-A*01:01; HLA-A*02:01; HLA-A*11:01; HLA-A*24:02; HLA-A*68:01; HLA-A*23:01; HLA-A*26:01; HLA-A*30:02; HLA-A*31:01; HLA-B*07:02; HLA-B*51:01; HLA-B*35:01; HLA-B*44:02; HLA-B*35:03; HLA-C*05:01; HLA-C*07:01 and HLA-C*15:02) in the Brazilian population.

Conclusions: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2.
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http://dx.doi.org/10.1136/jclinpath-2020-206946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409971PMC
August 2021

Housekeeping genes for RT-qPCR in ovine preimplantation embryos.

Zygote 2020 Jul 30:1-8. Epub 2020 Jul 30.

Departamento de Medicina Veterinária, Universidade Federal Rural de Pernambuco, Brazil.

Housekeeping genes (HKG) are paramount for accurate gene expression analysis during preimplantation development. Markedly, quantitative reverse transcription polymerase chain reaction (RT-qPCR) in ovine embryos currently lacks HKGs. Therefore, we tested 11 HKGs for RT-qPCR normalization during ovine parthenogenetic preimplantation development. Seven HKGs reached the qPCR efficiency threshold (97.20-105.96%), with correlation coefficients ranging from -0.922 to -0.998 and slopes from -3.22 to -3.59. GeNorm ranked glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and TATA-binding protein (TBP) as the best HKG pair, while H3 histone, family 3A (H3F3A) was the third HKG. Relative gene expression was measured for zinc finger protein X-linked (ZFX) and developmental pluripotency-associated 3 (DPPA3) transcripts during ovine parthenogenetic preimplantation development. ZFX did not show any transcript abundance fluctuation among oocytes, cleavage-stage embryos, and morulae. DPPA3 transcript abundance was also similar among all developmental stages, therefore suggesting that it may not display a maternal gene expression profile. In silico analysis of ovine DPPA3 mRNA and protein showed high conservation to bovine orthologues. However, DPPA3 orthologues differed in regulatory motifs. In conclusion, GAPDH, TBP and H3F3A are stable HKGs in ovine parthenogenetic embryos and allow accurate RT-qPCR-based gene expression analysis.
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http://dx.doi.org/10.1017/S0967199420000295DOI Listing
July 2020

Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris).

Chromosome Res 2020 12 11;28(3-4):293-306. Epub 2020 Jul 11.

Departamento de Genética, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.

Comparative cytogenetic mapping is a powerful approach to gain insights into genome organization of orphan crops, lacking a whole sequenced genome. To investigate the cytogenomic evolution of important Vigna and Phaseolus beans, we built a BAC-FISH (fluorescent in situ hybridization of bacterial artificial chromosome) map of Vigna aconitifolia (Vac, subgenus Ceratotropis), species with no sequenced genome, and compared with V. unguiculata (Vu, subgenus Vigna) and Phaseolus vulgaris (Pv) maps. Seventeen Pv BACs, eight Vu BACs, and 5S and 35S rDNA probes were hybridized in situ on the 11 Vac chromosome pairs. Five Vac chromosomes (Vac6, Vac7, Vac9, Vac10, and Vac11) showed conserved macrosynteny and collinearity between V. unguiculata and P. vulgaris. On the other hand, we observed collinearity breaks, identified by pericentric inversions involving Vac2 (Vu2), Vac4 (Vu4), and Vac3 (Pv3). We also detected macrosynteny breaks of translocation type involving chromosomes 1 and 8 of V. aconitifolia and P. vulgaris; 2 and 3 of V. aconitifolia and P. vulgaris; and 1 and 5 of V. aconitifolia and V. unguiculata. Considering our data and previous BAC-FISH studies, six chromosomes (1, 2, 3, 4, 5, and 8) are involved in major karyotype divergences between genera and five (1, 2, 3, 4, and 5) between Vigna subgenera, including mechanisms such as duplications, inversions, and translocations. Macrosynteny breaks between Vigna and Phaseolus suggest that the major chromosomal rearrangements have occurred within the Vigna clade. Our cytogenomic comparisons bring new light on the degree of shared macrosynteny and mechanisms of karyotype diversification during Vigna and Phaseolus evolution.
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http://dx.doi.org/10.1007/s10577-020-09635-0DOI Listing
December 2020

Genome composition and pollen viability of Jatropha (Euphorbiaceae) interspecific hybrids by Genomic In Situ Hybridization (GISH).

Genet Mol Biol 2020 31;42(4):e20190112. Epub 2020 Jan 31.

Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.

Interspecific hybridization is required for the development of Jatropha curcas L. improved cultivars, due to its narrow genetic basis. The present study aimed to analyze the parental genomic composition of F1 and BC1F1 generations derived from interspecific crosses (J. curcas/J. integerrima and J. curcas/J. multifida) by GISH (Genomic In Situ Hybridization), and the meiotic index and pollen viability of F1 hybrids. In F1 cells from both hybrids, 11 chromosomes of each parental was observed, as expected, but chromosome rearrangement events could be detected using rDNA chromosome markers, suggesting unbalanced cells. In the BC1F1, both hybrids had 22 chromosomes, suggesting that only n = 11 gametes were viable in the next generation. However, GISH allowed the identification of three and two alien chromosomes in J. curcas//J. integerrima and J. curcas//J. multifida BC1F1 hybrids, respectively, suggesting a preferential transmission of J. curcas chromosomes for both hybrids. Pollen viability in F1 hybrids derived from J. curcas/J. integerrima crosses were higher (82-83%) than those found for J. curcas/J. multifida (68%), showing post-meiotic problems in these last hybrids, with dyads, triads, polyads, and micronuclei as post-meiosis results. The here presented cytogenetic characterization of interspecific hybrids and their backcross progenies can contribute to the selection of the best genotypes for future assisted breeding of J. curcas.
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http://dx.doi.org/10.1590/1678-4685-GMB-2019-0112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198012PMC
January 2020

Gene isolation and structural characterization of a legume tree defensin with a broad spectrum of antimicrobial activity.

Planta 2019 Nov 19;250(5):1757-1772. Epub 2019 Aug 19.

Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay.

Main Conclusion: The recombinant EcgDf1 defensin has an antimicrobial effect against both plant and human pathogens. In silico analyses predict that EcgDf1 is prone to form dimers capable of interacting with the membranes of microorganisms. Plant defensins comprise a large family of antimicrobial peptides (AMP) with a wide range of biological functions. They are cysteine-rich molecules, highly sequence diverse but with a conserved and stable structure. In this work, a defensin gene (EcgDf1) was isolated from Erythrina crista-galli, a legume tree native from South America. The predicted peptide presents eight cysteines, with a γ-core motif GXCX3-9C and six cysteines distributed like the typical defensin αβ motif. The mature EcgDf1 coding sequence was heterologously expressed in Escherichia coli strains and purified by affinity chromatography. Possible dimer and oligomers of EcgDf1 were visible in SDS electrophoresis. Moreover, its 3D structure, determined by homology modeling, docking, and molecular dynamics simulations, was found to be compatible with the formation of homodimers between the β3 and β1-loop-α1, leaving the β2-loop-β3 free to interact with lipid membranes. The purified recombinant peptide inhibited the growth of several critical plant and human pathogens, like the opportunistic fungi Candida albicans and Aspergillus niger and the plant pathogens Clavibacter michiganensis ssp. michiganensis, Penicillium expansum, Botrytis cinerea, and Alternaria alternata. EcgDf1 is a promising candidate for the development of antimicrobial products for use in agriculture and medicine.
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http://dx.doi.org/10.1007/s00425-019-03260-wDOI Listing
November 2019

Reference genes selection for Calotropis procera under different salt stress conditions.

PLoS One 2019 18;14(4):e0215729. Epub 2019 Apr 18.

Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Fisiologia Vegetal, Recife, PE, Brazil.

Calotropis procera is a perennial Asian shrub with significant adaptation to adverse climate conditions and poor soils. Given its increased salt and drought stress tolerance, C. procera stands out as a powerful candidate to provide alternative genetic resources for biotechnological approaches. The qPCR (real-time quantitative polymerase chain reaction), widely recognized among the most accurate methods for quantifying gene expression, demands suitable reference genes (RGs) to avoid over- or underestimations of the relative expression and incorrect interpretation. This study aimed at evaluating the stability of ten RGs for normalization of gene expression of root and leaf of C. procera under different salt stress conditions and different collection times. The selected RGs were used on expression analysis of three target genes. Three independent experiments were carried out in greenhouse with young plants: i) Leaf100 = leaf samples collected 30 min, 2 h, 8 h and 45 days after NaCl-stress (100 mM NaCl); ii) Root50 and iii) Root200 = root samples collected 30 min, 2 h, 8 h and 1day after NaCl-stress (50 and 200 mM NaCl, respectively). Stability rank among the three algorithms used showed high agreement for the four most stable RGs. The four most stable RGs showed high congruence among all combination of collection time, for each software studied, with minor disagreements. CYP23 was the best RG (rank of top four) for all experimental conditions (Leaf100, Root50, and Root200). Using appropriated RGs, we validated the relative expression level of three differentially expressed target genes (NAC78, CNBL4, and ND1) in Leaf100 and Root200 samples. This study provides the first selection of stable reference genes for C. procera under salinity. Our results emphasize the need for caution when evaluating the stability RGs under different amplitude of variable factors.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0215729PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472812PMC
January 2020

Plant Thaumatin-like Proteins: Function, Evolution and Biotechnological Applications.

Curr Protein Pept Sci 2020 ;21(1):36-51

Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil.

Thaumatin-like proteins (TLPs) are a highly complex protein family associated with host defense and developmental processes in plants, animals, and fungi. They are highly diverse in angiosperms, for which they are classified as the PR-5 (Pathogenesis-Related-5) protein family. In plants, TLPs have a variety of properties associated with their structural diversity. They are mostly associated with responses to biotic stresses, in addition to some predicted activities under drought and osmotic stresses. The present review covers aspects related to the structure, evolution, gene expression, and biotechnological potential of TLPs. The efficiency of the discovery of new TLPs is below its potential, considering the availability of omics data. Furthermore, we present an exemplary bioinformatics annotation procedure that was applied to cowpea (Vigna unguiculata) transcriptome, including libraries of two tissues (root and leaf), and two stress types (biotic/abiotic) generated using different sequencing approaches. Even without using genomic sequences, the pipeline uncovered 56 TLP candidates in both tissues and stresses. Interestingly, abiotic stress (root dehydration) was associated with a high number of modulated TLP isoforms. The nomenclature used so far for TLPs was also evaluated, considering TLP structure and possible functions identified to date. It is clear that plant TLPs are promising candidates for breeding purposes and for plant transformation aiming a better performance under biotic and abiotic stresses. The development of new therapeutic drugs against human fungal pathogens also deserves attention. Despite that, applications derived from TLP molecules are still below their potential, as it is evident in our review.
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http://dx.doi.org/10.2174/1389203720666190318164905DOI Listing
January 2021

Karyotype heterogeneity in Philodendron s.l. (Araceae) revealed by chromosome mapping of rDNA loci.

PLoS One 2018 15;13(11):e0207318. Epub 2018 Nov 15.

Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, CEP, Recife, Pernambuco, Brazil.

Philodendron s.l. (Araceae) has been recently focus of taxonomic and phylogenetic studies, but karyotypic data are limited to chromosome numbers and a few published genome sizes. In this work, karyotypes of 34 species of Philodendron s.l. (29 species of Philodendron and five of Thaumatophyllum), ranging from 2n = 28 to 36 chromosomes, were analyzed by fluorescence in situ hybridization (FISH) with rDNA and telomeric probes, aiming to understand the evolution of the karyotype diversity of the group. Philodendron presented a high number variation of 35S rDNA, ranging from two to 16 sites, which were mostly in the terminal region of the short arms, with nine species presenting heteromorphisms. In the case of Thaumatophyllum species, we observed a considerably lower variation, which ranged from two to four terminal sites. The distribution of the 5S rDNA clusters was more conserved, with two sites for most species, being preferably located interstitially in the long chromosome arms. For the telomeric probe, while exclusively terminal sites were observed for P. giganteum (2n = 30) chromosomes, P. callosum (2n = 28) presented an interstitial distribution associated with satellite DNA. rDNA sites of the analyzed species of Philodendron s.l. species were randomly distributed considering the phylogenetic context, probably due to rapid evolution and great diversity of these genomes. The observed heteromorphisms suggest the accumulation of repetitive DNA in the genomes of some species and the occurrence of chromosomal rearrangements along the karyotype evolution of the group.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207318PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237374PMC
April 2019

Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR.

Plant Methods 2018 12;14:88. Epub 2018 Oct 12.

2Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil.

Background: Due to cowpea ability to fix nitrogen in poor soils and relative tolerance to drought and salt stresses, efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Real-time quantitative PCR (qPCR) has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. In the present study, nine candidate reference genes were rigorously tested for their application in normalization of qPCR data onto roots of four distinct cowpea accessions under two abiotic stresses: root dehydration and salt (NaCl, 100 mM). In addition, the regulation of four target transcripts, under the same referred conditions was also scrutinized.

Results: geNorm, NormFinder, BestKeeper, and ΔCt method results indicated a set of three statistically validated RGs for each stress condition: (I) root dehydration (actin, ubiquitin-conjugating enzyme E2 variant 1D, and a unknown gene-), and (II) salt (ubiquitin-conjugating enzyme E2 variant 1D, F-box protein, and ). The expression profile of the target transcripts suggests that flavonoids are important players in the cowpea response to the abiotic stresses analyzed, since chalcone isomerase and chalcone synthase were up-regulated in the tolerant and sensitive accessions. A lipid transfer protein also participates in the cowpea tolerance mechanisms to root dehydration and salt stress. The referred transcript was up-regulated in the two tolerant accessions and presented no differential expression in the sensitive counterparts. Chitinase B, in turn, generally related to plant defense, was an important target transcript under salt stress, being up-regulated at the tolerant, and down-regulated in the sensitive accession.

Conclusions: Reference genes suitable for qPCR analyses in cowpea under root dehydration and salt stress were identified. This action will lead to a more accurate and reliable analysis of gene expression on this species. Additionally, the results obtained in this study may guide future research on gene expression in cowpea under other abiotic stress types that impose osmotic imbalance. The target genes analyzed, in turn, deserve functional evaluation due to their transcriptional regulation under stresses and biotechnological potential.
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http://dx.doi.org/10.1186/s13007-018-0354-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182843PMC
October 2018

Antimicrobial and structural insights of a new snakin-like peptide isolated from Peltophorum dubium (Fabaceae).

Amino Acids 2018 Sep 8;50(9):1245-1259. Epub 2018 Jun 8.

Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, 11800, Montevideo, Uruguay.

Snakins are antimicrobial peptides (AMPs) found, so far, exclusively in plants, and known to be important in the defense against a wide range of pathogens. Like other plant AMPs, they contain several positively charged amino acids, and an even number of cysteine residues forming disulfide bridges which are considered important for their usual function. Despite its importance, studies on snakin tertiary structure and mode of action are still scarce. In this study, a new snakin-like gene was isolated from the native plant Peltophorum dubium, and its expression was verified in seedlings and adult leaves. The deduced peptide (PdSN1) shows 84% sequence identity with potato snakin-1 mature peptide, with the 12 cysteines characteristic from this peptide family at the GASA domain. The mature PdSN1 coding sequence was successfully expressed in Escherichia coli. The purified recombinant peptide inhibits the growth of important plant and human pathogens, like the economically relevant potato pathogen Streptomyces scabies and the opportunistic fungi Candida albicans and Aspergillus niger. Finally, homology and ab initio modeling techniques coupled to extensive molecular dynamics simulations were used to gain insight on the 3D structure of PdSN1, which exhibited a helix-turn-helix motif conserved in both native and recombinant peptides. We found this motif to be strongly coded in the sequence of PdSN1, as it is stable under different patterns of disulfide bonds connectivity, and even when the 12 cysteines are considered in their reduced form, explaining the previous experimental evidences.
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http://dx.doi.org/10.1007/s00726-018-2598-3DOI Listing
September 2018

Karyotype and genome size comparative analyses among six species of the oilseed-bearing genus Jatropha (Euphorbiaceae).

Genet Mol Biol 2018 Apr./Jun;41(2):442-449. Epub 2018 May 14.

Department of Genetics, Universidade Federal de Pernambuco, Recife, PE, Brazil.

Jatropha is an important genus of Euphorbiaceae, with species largely used for various purposes, including the manufacturing of soaps and pharmaceutical products and applications in the bioenergetic industry. Although there have been several studies focusing J. curcas in various aspects, the karyotype features of Jatropha species are poorly known. Therefore, we analyzed six Jatropha species through fluorochrome staining (CMA/DAPI), fluorescent in situ hybridization (FISH) with 5S and 45S rDNA probes and genome size estimation by flow cytometry. Our results revealed several chromosome markers by both CMA/DAPI and FISH for the analyzed species. Five Jatropha species (J. curcas, J. gossypiifolia, J. integerrima, J. multifida and J. podagrica) showed four CMA-positive (CMA+) bands associated with the 5S and 45S rDNA sites (one and two pairs, respectively). However, J. mollissima displayed six CMA+/DAPI- bands co-localized with both 5S and 45S rDNA, which showed a FISH superposition. A gradual variation in the genome sizes was observed (2C = 0.64 to 0.86 pg), although an association between evidenced heterochromatin and genome sizes was not found among species. Except for the unique banding pattern of J. mollissima and the pericentromeric heterochromatin of J. curcas and J. podagrica, our data evidenced relatively conserved karyotypes.
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http://dx.doi.org/10.1590/1678-4685-GMB-2017-0120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082239PMC
May 2018

Recognition of the genus Schott - formerly Philodendron subg. Meconostigma (Araceae) - based on molecular and morphological evidence.

PhytoKeys 2018 2(98):51-71. Epub 2018 May 2.

Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.

Philodendron subgenus Meconostigma has been a well-circumscribed group since 1829. Members of this group are easily distinguished by diagnostic morphological characters as well as by a distinct ecology and geographical distribution. Based on molecular, morphological and cytological evidence, we propose the recognition of P. subg. Meconostigma as a distinct genus, Schott. We also present the necessary new combinations, an emended key and some nomenclatural and taxonomic corrections regarding 21 names of .
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http://dx.doi.org/10.3897/phytokeys.98.25044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943393PMC
May 2018

Complete Genome Sequence of pv. Strain IBSBF2579 from Brazil.

Genome Announc 2018 Feb 1;6(5). Epub 2018 Feb 1.

Department of Agronomy, Federal Rural University of Pernambuco, Recife, Brazil

The bacterium pv. is the agent of angular leaf spot of the cashew tree ( L.). The complete genome sequencing of the strain IBSBF2579 was done on an Illumina HiSeq 2500 platform. The assembly of the pv. strain IBSBF2579 genome yielded 133 contigs, with a size of 5,329,247 bp and a G+C content of 64.03%. The prediction was performed by GeneMarkS and the automatic annotation by Rapid Annotations using Subsystems Technology (RAST), with 4,406 identified genes.
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http://dx.doi.org/10.1128/genomeA.01574-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794958PMC
February 2018

Draft genome assembly of , the pathogen of banana fruit.

Data Brief 2018 Apr 8;17:256-260. Epub 2018 Jan 8.

Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, PE, Brazil.

is an important cosmopolitan pathogenic fungus that causes anthracnose in banana fruit. The entire genome of isolate GM20 (CMM 4420), originally isolated from infected banana fruit from Alagoas State, Brazil, was sequenced and annotated. The pathogen genomic DNA was sequenced on HiSeq Illumina platform. The GM20 genome has 50,635,197 bp with G + C content of 53.74% and in its present assembly has 2763 scaffolds, harboring 13,451 putative genes with an average length of 1626 bp. Gene prediction and annotation was performed by Funannotate pipeline, using a pattern for gene identification based on BUSCO.
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http://dx.doi.org/10.1016/j.dib.2018.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790810PMC
April 2018

Editorial: Plant Immunity and Beyond: Signals from Proteins & Peptides.

Curr Protein Pept Sci 2017;18(4):292-293

Universidade Federal de Pernambuco Genetics Department, Center of Biological Sciences Av. Prof. Moraes Rego, 1235, 50.670-423 Recife, Pernambuco. Brazil.

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http://dx.doi.org/10.2174/138920371804170206201325DOI Listing
August 2018
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