DEAD-Box RNA Helicase Family in Physic Nut (Jatropha curcas L.): Structural Characterization and Response to Salinity.

Helicases, motor proteins present in both prokaryotes and eukaryotes, play a direct role in various steps of RNA metabolism. Specifically, SF2 RNA helicases, a subset of the DEAD-box family, are essential players in plant developmental processes and responses to biotic and abiotic stresses. Despite this, information on this family in the physic nut (Jatropha curcas L.) remains limited, spanning from structural patterns to stress responses. We identified 79 genes encoding DEAD-box RNA helicases (JcDHX) in the J. curcas genome. These genes were further categorized into three subfamilies: DEAD (42 genes), DEAH (30 genes), and DExH/D (seven genes). Characterization of the encoded proteins revealed a remarkable diversity, with observed patterns in domains, motifs, and exon-intron structures suggesting that the DEAH and DExH/D subfamilies in J. curcas likely contribute to the overall versatility of the family. Three-dimensional modeling of the candidates showed characteristic hallmarks, highlighting the expected functional performance of these enzymes. The promoter regions of the JcDHX genes revealed potential cis-elements such as Dof-type, BBR-BPC, and AP2-ERF, indicating their potential involvement in the response to abiotic stresses. Analysis of RNA-Seq data from the roots of physic nut accessions exposed to 150 mM of NaCl for 3 h showed most of the JcDHX candidates repressed. The protein-protein interaction network indicated that JcDHX proteins occupy central positions, connecting events associated with RNA metabolism. Quantitative PCR analysis validated the expression of nine DEAD-box RNA helicase transcripts, showing significant associations with key components of the stress response, including RNA turnover, ribosome biogenesis, DNA repair, clathrin-mediated vesicular transport, phosphatidyl 3,5-inositol synthesis, and mitochondrial translation. Furthermore, the induced expression of one transcript (JcDHX44) was confirmed, suggesting that it is a potential candidate for future functional analyses to better understand its role in salinity stress tolerance. This study represents the first global report on the DEAD-box family of RNA helicases in physic nuts and displays structural characteristics compatible with their functions, likely serving as a critical component of the plant's response pathways.

Cytomolecular diversity among Vigna Savi (Leguminosae) subgenera.

The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus.

Translocations and inversions: major chromosomal rearrangements during Vigna (Leguminosae) evolution.

KEY MESSAGE: Inversions and translocations are the major chromosomal rearrangements involved in Vigna subgenera evolution, being Vigna vexillata the most divergent species. Centromeric repositioning seems to be frequent within the genus. Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH) provides a powerful chromosome identification system for inferring plant chromosomal evolution. Aiming to understand macrosynteny, chromosomal diversity, and the evolution of bean species from five Vigna subgenera, we constructed cytogenetic maps for eight taxa using oligo-FISH-based chromosome identification. We used oligopainting probes from chromosomes 2 and 3 of Phaseolus vulgaris L. and two barcode probes designed from V. unguiculata (L.) Walp. genome. Additionally, we analyzed genomic blocks among the Ancestral Phaseoleae Karyotype (APK), two V. unguiculata subspecies (V. subg. Vigna), and V. angularis (Willd.) Ohwi & Ohashi (V. subg. Ceratotropis). We observed macrosynteny for chromosomes 2, 3, 4, 6, 7, 8, 9, and 10 in all investigated taxa except for V. vexillata (L.) A. Rich (V. subg. Plectrotropis), in which only chromosomes 4, 7, and 9 were unambiguously identified. Collinearity breaks involved with chromosomes 2 and 3 were revealed. We identified minor differences in the painting pattern among the subgenera, in addition to multiple intra- and interblock inversions and intrachromosomal translocations. Other rearrangements included a pericentric inversion in chromosome 4 (V. subg. Vigna), a reciprocal translocation between chromosomes 1 and 5 (V. subg. Ceratotropis), a potential deletion in chromosome 11 of V. radiata (L.) Wilczek, as well as multiple intrablock inversions and centromere repositioning via genomic blocks. Our study allowed the visualization of karyotypic patterns in each subgenus, revealing important information for understanding intrageneric karyotypic evolution, and suggesting V. vexillata as the most karyotypically divergent species.

Unlocking Cowpea's Defense Responses: Conserved Transcriptional Signatures in the Battle against CABMV and CPSMV Viruses.

Cowpea aphid-borne mosaic virus (CABMV) and Cowpea severe mosaic virus (CPSMV) threaten cowpea commercial production. This study aimed to analyze Conserved Transcriptional Signatures (CTS) in cowpea's genotypes that are resistant to these viruses. CTS covered up- (UR) or down-regulated (DR) cowpea transcripts in response to CABMV and CPSMV mechanical inoculations. The conservation of cowpea's UR defense response was primarily observed with the one hpi treatments, with decreased CTS representatives as time elapsed. This suggests that cowpea utilizes generic mechanisms during its early interaction with the studied viruses, and subsequently employs more specialized strategies for each viral agent. The potential action of the CTS-UR emphasizes the importance of redox balance, ethylene and jasmonic acid pathways. Additionally, the CTS-UR provides evidence for the involvement of R genes, PR proteins, and PRRs receptors-extensively investigated in combating bacterial and fungal pathogens-in the defense against viral inoculation. AP2-ERF, WRKY, and MYB transcription factors, as well as PIP aquaporins and MAPK cascades, also emerged as significant molecular players. The presented work represents the first study investigating conserved mechanisms in the cowpea defense response to viral inoculations, highlighting relevant processes for initial defense responses.

AMMI-Bayesian perspective in the selection of pre-cultivars of carioca beans in Agreste-Sertão of Pernambuco, Brazil.

The productivity of beans is greatly influenced by the different edaphoclimatic conditions in the Agreste-Sertão region, requiring the identification of adapted and stable genotypes to minimize the effects of the interaction between genotypes per environments (GxE). The objective of this work was to analyze the adaptability and stability of carioca bean pre-cultivars in three municipalities in the Agreste-Sertão of Pernambuco using the AMMI model in its Bayesian version BAMMI and compare the results with the frequentist approach. According to the results, the BAMMI analysis showed better predictive capacity, as well as better performance in the study of adaptability and stability. The cultivar BRS Notável stood out in terms of main effect and stability. Adaptability of genotypes to specific locations was also observed, enabling the use of the positive effect of the GxE interaction, which was more evident with the BAMMI model. From this work, the flexibility of BAMMI model to deal with data resulting from multi-environmental experiments can be seen, overcoming limitations of the standard analysis of the AMMI model.

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

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.

Evaluation of Mycotoxin Production and Phytopathogenicity of the Entomopathogenic Fungi Fusarium caatingaense and F. pernambucanum from Brazil.

Fusarium incarnatum-equiseti species complex (FIESC) is considered as one of the richest insecticolous species. Fusarium species synthesize toxic secondary metabolites that are not fully understood. Mycotoxin production and pathogenicity on germinating seeds, seedlings, and leaves must be carefully studied for the use of Fusarium species in the biological control of insect pests. In this study, we evaluated the mycotoxin production and phytopathogenic potential of entomopathogenic strains of Fusarium sulawesiensis (1), F. pernambucanum (3), and F. caatingaense (23). The phytopathogenicity tests of F. caatingaense (URM 6776, URM 6777, URM 6778, URM 6779, and URM 6782) were performed during the development of bean (Phaseolus vulgaris, Vigna unguiculata, and Phaseolus lunatus), and corn (Zea mays) seedlings, using four treatments (soil infestation with the inoculum, spraying on leaves, root dip, and negative control). The mycotoxins, monoacetyl-deoxynivalenols (AcDON), deoxynivalenol (DON), beauvericin (BEA), fusarenone-X (FUS), T-2 toxin (T2), diacetoxyscirpenol (DAS), and zearalenone (ZEA), were detected in the study; BEA (detected in 25 strains) and FUS (detected in 21 strains) were found to be predominant. None of the strains showed any ability to cause disease or virulence in beans and corn. The FIESC strains showed a highly variable production of mycotoxins without the potential to be used as phytopathogenic agents for the cultures tested.

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil.

Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.

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

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.

Morphology, phylogeny, and sexual stage of Fusarium caatingaense and Fusarium pernambucanum, new species of the Fusarium incarnatum-equiseti species complex associated with insects in Brazil.

Based on morphological and molecular phylogenetic markers and the fertility of sexual crosses, two novel species of Fusarium associated with Dactylopius opuntiae (Hemiptera: Dactylopiidae) and Aleurocanthus woglumi (Hemiptera: Aleyrodidae) from northeastern Brazil are described as Fusarium caatingaense and F. pernambucanum. Partial sequences of five loci were generated for 29 entomopathogenic Fusarium isolates. Multilocus phylogenetic analyses demonstrated that F. caatingaense and F. pernambucanum belong to the Incarnatum clade of the Fusarium incarnatum-equiseti species complex (FIESC). These species displayed common morphological characters such as the production of various types of aerial conidia formed on monophialides and polyphialides and differ from each other mainly in the dimensions and morphology of their sporodochial conidia. Mating type polymerase chain reaction (PCR) revealed 17 MAT1-1 isolates and 12 MAT1-2 isolates, all of them heterothallic. Fertile perithecia were produced in 4.2% of infraspecific crosses of F. caatingaense and in 13.3% of infraspecific crosses of F. pernambucanum after 2-3 wk. Crosses between F. caatingaense and F. pernambucanum did not result in fertile perithecia. We demonstrate the existence of a sexual stage in species of the Incarnatum clade and describe the morphological characters of these sexual morphs for the first time. These results suggest that previously unknown sexual cycles contribute to the high genetic diversity within FIESC.

Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH.

Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes.

Interrelationship of Bradyrhizobium sp. and plant growth-promoting bacteria in cowpea: survival and symbiotic performance.

The objective of this study was to evaluate the survival of cowpea during bacterial colonization and evaluate the interrelationship of the Bradyrhizobium sp. and plant growth-promoting bacteria (PGPB) as a potential method for optimizing symbiotic performance and cowpea development. Two experiments using the model legume cowpea cv. "IPA 206" were conducted. In the first experiment, cowpea seeds were disinfected, germinated and transferred to sterilized Gibson tubes containing a nitrogen-free nutritive solution. The experimental design was randomized blocks with 24 treatments [Bradyrhizobium sp. (BR 3267); 22 PGPB; absolute control (AC)] with three replicates. In the second experiment, seeds were disinfected, inoculated according to their specific treatment and grown in Leonard jars containing washed and autoclaved sand. The experimental design was randomized blocks with 24 treatments [BR 3267; 22 BR 3267 + PGPB; AC] with three replicates. Scanning electron microscopy demonstrated satisfactory colonization of the roots of inoculated plants. Additionally, synergism between BR 3267 and PGPB in cowpeas was observed, particularly in the BR 3267 + Paenibacillus graminis (MC 04.21) and BR 3267 + P. durus (C 04.50), which showed greater symbiotic performance and promotion of cowpea development.