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Purpose: This study aims to identify nurses' concerns about the clinical, ethical, and legal aspects of deactivating cardiovascular implantable electronic devices (CIEDs).Methods: We used focus groups to discuss decision making in CIED management.Results: Fourteen nurses described the informed consent process as overly focused on procedures, with inadequate coverage of living with a device (e.g., infection risks and device shocks). Elderly patients were especially vulnerable to physician or family pressure about CIED implantation. Nurses believed that initial advance care planning discussions were infrequent and rarely revisited when health status changed. Many patients did not know that CIEDs could be deactivated; it was often addressed reactively (i.e., after multiple shocks) or when patients became too ill to participate in decision making. Nurses generally were supportive of CIED deactivation when it was requested by a well-informed patient. However, nurses distinguished between withholding versus withdrawing treatment (i.e., turning off CIEDs vs. declining implantation). Although most patients viewed their device as lifesaving, others perceived them as a "ticking time bomb."Conclusions: Nurses identified concerns about CIED decision making from implantation through end-of-life care and device deactivation and suggested avenues for improving patient care including early and regular advance care planning. [ABSTRACT FROM AUTHOR]

Background: As a follow-up of a previously reported three-year study, we analyzed the periprosthetic acetabular cortical and cancellous bone density changes at ten years after implantation of a press-fit cup.Methods: Prospective clinical, radiographic, and quantitative computed tomography examinations were performed within ten days and at mean periods of one, three, and ten years after total hip arthroplasty with a press-fit cup, a femoral stem with a tapered design, and alumina-alumina pairing. Periacetabular cortical and cancellous bone density (mg CaHA/mL) in the cranial, ventral, and dorsal regions about the cup were measured for twenty-four hips in vivo.Results: All acetabular cups showed radiographic signs of stable ingrowth, and no acetabular component had to be revised. The loss of periacetabular cancellous bone density about the cup was as much as -37% cranially, -60% ventrally, and -71% dorsally; the decrease was progressive between the one-year and three-year examinations only. In contrast, cortical bone density above the dome of the acetabular cup remained constant throughout the ten-year follow-up. A moderate change in cortical bone density of -5% to -18% was seen at the level of the cup ten years postoperatively.Conclusions: Both periacetabular cortical and cancellous bone density changes were nonprogressive between the three-year and ten-year examinations after press-fit cup fixation. [ABSTRACT FROM AUTHOR]

Background Aseptic implant loosening and periprosthetic bone loss are major problems after total hip arthroplasty (THA). We present an in vivo method of computed tomography (CT) assisted osteodensitometry after THA that differentiates between cortical and cancellous bone density (BD) and area around the femoral component. Method Cortical and cancellous periprosthetic femoral BD (mg CaHA/mL), area (mm2) and contact area between the prothesis and cortical bone were determined prospectively in 31 patients 10 days, 1 year, and 6 years after uncemented THA (mean age at implantation: 55 years) using CT-osteodensitometry. Results 6 years postoperatively, cancellous BD had decreased by as much as 41% and cortical BD by up to 27% at the metaphyseal portion of the femur; this decrease was progressive between the 1-year and 6-year examinations. Mild cortical hypertrophy was observed along the entire length of the diaphysis. No statistically significant changes in cortical BD were observed along the diaphysis of the stem. Interpretation Periprosthetic CT-assisted osteodensitometry has the technical ability to discriminate between cortical and cancellous bone structures with respect to strain-adapted remodeling. Continuous loss of cortical and cancellous BD at the femoral metaphysis, a homeostatic cortical strain configuration, and mild cortical hypertrophy along the diaphysis suggest a diaphyseal fixation of the implanted stem. CT-assisted osteodensitometry has the potential to become an effective instrument for quality control in THA by means of in vivo determination of periprosthetic BD, which may be a causal factor in implant loosening after THA. [ABSTRACT FROM AUTHOR]

Periprosthetic bone loss after total hip arthroplasty is common. It can be progressive and, in the extreme, may compromise survival of the prosthesis. With quantitative computed tomography, we determined the pattern of periacetabular cortical and cancellous bone density changes after press-fit cup implantation with alumina liners. We recruited 24 patients (24 hips; 15 men and nine women) with degenerative joint disease and used a press-fit cup with an alumina/alumina pairing. The average patient age was 57 years. Computed tomography examinations were performed 10 days, 1 year, and 3 years after the index operation. Cancellous bone density decreased in all periacetabular regions by as much as -66%; the decrease was progressive between the 1- and 3-year examinations. In contrast, cortical bone density above the dome of the cup remained constant but progressively decreased by as much as -22% at the level of the cup 3 years postoperatively. Within the first 3 postoperative years, progressive periacetabular remodeling of cancellous and cortical bone structures was observed after press-fit cup fixation. The bone density changes suggest high stress shielding of retroacetabular cancellous bone while load is transmitted solely to the cortical bone above the dome of the cup. [ABSTRACT FROM AUTHOR]

Abstract Background Structural measures for networks have been extensively developed, but many of them have not yet demonstrated their sustainably. That means, it remains often unclear whether a particular measure is useful and feasible to solve a particular problem in network biology. Exemplarily, the classification of complex biological networks can be named, for which structural measures are used leading to a minimal classification error. Hence, there is a strong need to provide freely available software packages to calculate and demonstrate the appropriate usage of structural graph measures in network biology. Results Here, we discuss topological network descriptors that are implemented in the R-package QuACN and demonstrate their behavior and characteristics by applying them to a set of example graphs. Moreover, we show a representative application to illustrate their capabilities for classifying biological networks. In particular, we infer gene regulatory networks from microarray data and classify them by methods provided by QuACN. Note that QuACN is the first freely available software written in R containing a large number of structural graph measures. Conclusion The R package QuACN is under ongoing development and we add promising groups of topological network descriptors continuously. The package can be used to answer intriguing research questions in network biology, e.g., classifying biological data or identifying meaningful biological features, by analyzing the topology of biological networks.

Abstract Background Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological information about the underlying metabolic networks. These networks have been shown to share domain-independent structural similarities, which pose a special challenge for our endeavour. We quantify specific structural information by using topological network descriptors to classify this set of metabolic networks. Such measures quantify the structural complexity of the underlying networks. In this study, we use such measures to capture domain-specific structural features of the metabolic networks to classify the data set. So far, it has been a challenging undertaking to examine what kind of structural complexity such measures do detect. In this paper, we apply two groups of topological network descriptors to metabolic networks and evaluate their classification performance. Moreover, we combine the two groups to perform a feature selection to estimate the structural features with the highest classification ability in order to optimize the classification performance. Results By combining the two groups, we can identify seven topological network descriptors that show a group-specific characteristic by ANOVA. A multivariate analysis using feature selection and supervised machine learning leads to a reasonable classification performance with a weighted F-score of 83.7% and an accuracy of 83.9%. We further demonstrate that our approach outperforms alternative methods. Also, our results reveal that entropy-based descriptors show the highest classification ability for this set of networks. Conclusions Our results show that these particular topological network descriptors are able to capture domain-specific structural characteristics for classifying metabolic networks between the three domains of life.

Potato (Solanum tuberosum) is an essential crop for food security and is ranked as the third most important crop worldwide for human consumption. The Diacol Capiro cultivar holds the dominant position in Colombian cultivation, primarily catering to the food processing industry. This highly heterozygous, autotetraploid cultivar belongs to the Andigenum group and it stands out for its adaptation to a wide variety of environments spanning altitudes from 1,800 to 3,200 meters above sea level. Here, a chromosome-scale assembly, referred to as DC, is presented for this cultivar. The assembly was generated by combining circular consensus sequencing with proximity ligation Hi-C for the scaffolding and represents 2.369 Gb with 48 pseudochromosomes covering 2,091 Gb and an anchor rate of 88.26%. The reference genome metrics, including an N50 of 50.5 Mb, a BUSCO (Benchmarking Universal Single-Copy Orthologue) score of 99.38%, and an Long Terminal Repeat Assembly Index score of 13.53, collectively signal the achieved high assembly quality. A comprehensive annotation yielded a total of 154,114 genes, and the associated BUSCO score of 95.78% for the annotated sequences attests to their completeness. The number of predicted NLR (Nucleotide-Binding and Leucine-Rich-Repeat genes) was 2107 with a large representation of NBARC (for nucleotide binding domain shared by Apaf-1, certain R gene products, and CED-4) containing domains (99.85%). Further comparative analysis of the proposed annotation-based assembly with high-quality known potato genomes, showed a similar genome metrics with differences in total gene numbers related to the ploidy status. The genome assembly and annotation of DC presented in this study represent a valuable asset for comprehending potato genetics. This resource aids in targeted breeding initiatives and contributes to the creation of enhanced, resilient, and more productive potato varieties, particularly beneficial for countries in Latin America., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

The 5-year project 'Breeding roots, tubers and banana products for end user preferences' (RTBfoods) focused on collecting consumers' preferences on 12 food products to guide breeding programmes. It involved multidisciplinary teams from Africa, Latin America, and Europe. Diverse data types were generated on preferred qualities of users (farmers, family and entrepreneurial processors, traders or retailers, and consumers). Country-based target product profiles were produced with a comprehensive market analysis, disaggregating gender's role and preferences, providing prioritised lists of traits for the development of new plant varieties. We describe the approach taken to create, in the roots, tubers, and banana breeding databases, a centralised and meaningful open access to sensory information on food products and genotypes. Biochemical, instrumental textural, and sensory analysis data are then directly connected to the specific plant record while user survey data, bearing personal information, were analysed, anonymised, and uploaded in a repository. Names and descriptions of food quality traits were added into the Crop Ontology for labelling data in the databases, along with the various methods of measurement used by the project. The development and application of standard operating procedures, data templates, and adapted trait ontologies improved the data quality and its format, enabling the linking of these to the plant material studied when uploaded in the breeding databases or in repositories. Some modifications to the database model were necessary to accommodate the food sensory traits and sensory panel trials. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry., (© 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.)

Design randomizations and spatial corrections have increased understanding of genotypic, spatial, and residual effects in field experiments, but precisely measuring spatial heterogeneity in the field remains a challenge. To this end, our study evaluated approaches to improve spatial modeling using high-throughput phenotypes (HTP) via unoccupied aerial vehicle (UAV) imagery. The normalized difference vegetation index was measured by a multispectral MicaSense camera and processed using ImageBreed. Contrasting to baseline agronomic trait spatial correction and a baseline multitrait model, a two-stage approach was proposed. Using longitudinal normalized difference vegetation index data, plot level permanent environment effects estimated spatial patterns in the field throughout the growing season. Normalized difference vegetation index permanent environment were separated from additive genetic effects using 2D spline, separable autoregressive models, or random regression models. The Permanent environment were leveraged within agronomic trait genomic best linear unbiased prediction either modeling an empirical covariance for random effects, or by modeling fixed effects as an average of permanent environment across time or split among three growth phases. Modeling approaches were tested using simulation data and Genomes-to-Fields hybrid maize (Zea mays L.) field experiments in 2015, 2017, 2019, and 2020 for grain yield, grain moisture, and ear height. The two-stage approach improved heritability, model fit, and genotypic effect estimation compared to baseline models. Electrical conductance and elevation from a 2019 soil survey significantly improved model fit, while 2D spline permanent environment were most strongly correlated with the soil parameters. Simulation of field effects demonstrated improved specificity for random regression models. In summary, the use of longitudinal normalized difference vegetation index measurements increased experimental accuracy and understanding of field spatio-temporal heterogeneity., Competing Interests: Conflicts of interest: The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Mango ( Mangifera indica L.) (2n = 40) is a member of the Anacardiaceae family, which was domesticated at least 4000 years ago in Asia. Mangoes are delicious fruits with great nutritional value. They are one of the major fruit crops worldwide, cultivated in more than 100 countries, with a production of more than 40 million tons. Recently the genome sequences of several mango varieties have been released, but there are no bioinformatics platforms dedicated to mango genomics and breeding to host mango omics data. Here, we present MangoBase, a web portal dedicated to mango genomics, which provides multiple interactive bioinformatics tools, sequences, and annotations to analyze, visualize, and download omics data related to mango. Additionally, MangoBase includes a gene expression atlas with 12 datasets and 80 experiments representing some of the most significant mango RNA-seq experiments published to this date. These experiments study mango fruit ripening in several cultivars with different pulp firmness and sweetness or peel coloration, and other experiments also study hot water postharvest treatment, infection with C. gloeosporioides , and the main mango tree organ tissues.

Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress. In addition, we compared transcriptional changes in fruit with those in leaves to highlight different and conserved transcriptome signatures in vegetative and reproductive organs. We observed extensive and diverse genetic reprogramming in different fruit tissues and leaves, each associated with a unique response to drought acclimation. These included major transcriptional shifts in the placenta of growing fruit and in the seeds of ripe fruit related to cell growth and epigenetic regulation, respectively. Changes in metabolic and hormonal pathways, such as those related to starch, carotenoids, jasmonic acid, and ethylene metabolism, were associated with distinct fruit tissues and developmental stages. Gene coexpression network analysis provided further insights into the tissue-specific regulation of distinct responses to water stress. Our data highlight the spatiotemporal specificity of drought responses in tomato fruit and indicate known and unrevealed molecular regulatory mechanisms involved in drought acclimation, during both vegetative and reproductive stages of development., (© American Society of Plant Biologists 2022. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The tomato (Solanum lycopersicum L.) family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species [e.g., Jaltomata sinuosa (Miers) Mione and Nicotiana attenuata Torr. ex S. Watson]. Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum (Lindl.) M. L. Green, a woody lineage from the tomatillo (Physalis philadelphica Lam.) subfamily Physalideae. The assembled size of the genome (2.7 Gb) is more similar in size to pepper (Capsicum annuum L.) (2.6 Gb) than to other sequenced diploid members of the berry clade of Solanaceae [e.g., potato (Solanum tuberosum L.), tomato, and Jaltomata]. Our assembly recovers 92% of the conserved orthologous set, suggesting a nearly complete genome for this species. Most of the genomic content is repetitive (69%), with Gypsy elements alone accounting for 52% of the genome. Despite the large amount of repetitive content, most of the 12 I. cyaneum chromosomes are highly syntenic with tomato. Bayesian concordance analysis provides strong support for the berry clade, including I. cyaneum, but reveals extensive discordance along the backbone, with placement of chili pepper and Jaltomata being highly variable across gene trees. The I. cyaneum genome contributes to a growing wealth of genomic resources in Solanaceae and underscores the need for expanded sampling of diverse berry genomes to dissect major morphological transitions., (© 2022 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate., (© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Key Message: We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years., (© 2021. The Author(s).)

Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrated the microbial and chemical microenvironment of a patient's ileal mucosa with their clinical phenotype and genotype to identify factors favoring the growth and virulence of adherent and invasive E. coli (AIEC) linked to Crohn's disease. We determined that the ileal niche of AIEC was characterized by inflammation, dysbiosis, coculture of Enterococcus, and oxidative stress. We discovered that mucosal metabolites supported general growth of ileal E. coli, with a selective effect of ethanolamine on AIEC that was augmented by cometabolism of ileitis-associated amino acids and glutathione and by symbiosis-associated fucose. This metabolic plasticity was facilitated by the eut and pdu microcompartments, amino acid metabolism, γ-glutamyl-cycle, and pleiotropic stress responses. We linked metabolism to virulence and found that ethanolamine and glutamine enhanced AIEC motility, infectivity, and proinflammatory responses in vitro. We connected use of ethanolamine to intestinal inflammation and L-fuculose phosphate aldolase (fucA) to symbiosis in AIEC monoassociated IL10-/- mice. Collectively, we established that AIEC were pathoadapted to utilize mucosal metabolites associated with health and inflammation for growth and virulence, enabling the transition from symbiont to pathogen in a susceptible host.

Background: Huanglongbing, a devastating disease of citrus, is caused by the obligate, intracellular bacterium "Candidatus Liberibacter asiaticus" (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid. Development of transmission-blocking strategies to manage huanglongbing relies on knowledge of CLas and D. citri interactions at the molecular level. Prior transcriptome analyses of D. citri point to changes in psyllid biology due to CLas infection but have been hampered by incomplete versions of the D. citri genome, proper host plant controls, and/or a lack of a uniform data analysis approach. In this work, we present lessons learned from a quantitative transcriptome analysis of excised heads, salivary glands, midguts, and bacteriomes from CLas-positive and CLas-negative D. citri using the chromosomal length D. citri genome assembly., Results: Each organ had a unique transcriptome profile and response to CLas infection. Though most psyllids were infected with the bacterium, CLas-derived transcripts were not detected in all organs. By analyzing the midgut dataset using both the Diaci_v1.1 and v3.0 D. citri genomes, we showed that improved genome assembly led to significant and quantifiable differences in RNA-sequencing data interpretation., Conclusions: Our results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue-specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

Hox genes and their cofactors are essential developmental genes specifying regional identity in animals. Hox genes have a conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. A few insect species have breaks in the cluster, but these are exceptions. We annotated the 10 Hox genes of the Asian citrus psyllid Diaphorina citri , and found a split in its Hox cluster between the Deformed and Sex combs reduced genes - the first time a break at this position has been observed in an insect Hox cluster. We also annotated D. citri orthologs of the Hox cofactor genes homothorax, PKNOX and extradenticle and found an additional copy of extradenticle in D. citri that appears to be a retrogene. Expression data and sequence conservation suggest that the extradenticle retrogene may have retained the original extradenticle function and allowed divergence of the parental extradenticle gene., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of Diaphorina citri, the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Candidatus Liberibacter asiaticus ( C Las), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on cry1 and cry2 identified in the psyllid genome, D. citri likely possesses a circadian model similar to the lepidopteran butterfly, Danaus plexippus . Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

Objective: The redbanded stink bug (RBSB), Piezodorus guildinii (Hemiptera: Pentatomidae), is native to the Caribbean Basin and is currently considered an invasive pest in Florida, Louisiana, Mississippi, and Texas in the southern United States. Although RBSB is an economically important invasive pest in the USA, relatively few studies have been conducted to understand molecular mechanisms, population genetic structure, and the genetic basis of resistance to insecticides. The objective of this work was to obtain a high-quality genome assembly to develop genomic resources to conduct population genetic, genomic, and physiological studies of the RBSB., Results: The genome of RBSB was sequenced with Pacific Biosciences technology followed by two rounds of scaffolding using Chicago libraries and HiC proximity ligation to obtain a high-quality assembly. The genome assembly contained 800 scaffolds larger than 1 kbp and the N50 was 170.84 Mbp. The largest scaffold was 222.22 Mbp and 90% of the genome was included in the 7 scaffolds larger than 118 Mbp. The number of megabase scaffolds also matched the number of chromosomes in this insect. The genome sequence will facilitate the development of resources to conduct studies on genetics, transcriptomics, and physiology of RBSB., (© 2022. The Author(s).)

Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri , carries the bacterium causing Huanglongbing, or citrus greening disease, a devastating citrus disease. We identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high-quality gene models to aid the design of interdictory molecules for pest control. We categorized the D. citri chitinases according to an established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases from known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

Ubiquitination is an ATP-dependent process that targets proteins for degradation by the proteasome. Here, we annotated 15 genes from the ubiquitin-proteasome pathway in the Asian citrus psyllid, Diaphorina citri . This psyllid vector has come to prominence in the last decade owing to its role in the transmission of the devastating bacterial pathogen, Candidatus Liberibacter asiaticus ( C Las). Infection of citrus crops by this pathogen causes Huanglongbing (HLB), or citrus greening disease, and results in the eventual death of citrus trees. The identification and correct annotation of these genes in D. citri will be useful for functional genomic studies to aid the development of RNAi-based management strategies aimed at reducing the spread of HLB. Investigating the effects of C Las infection on the expression of ubiquitin-proteasome pathway genes may provide new information about the role these genes play in the acquisition and transmission of C Las by D. citri ., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

Citrus greening disease is caused by the pathogen Candidatus Liberibacter asiaticus and transmitted by the Asian citrus psyllid, Diaphorina citri . No curative treatment or significant prevention mechanism exists for this disease, which causes economic losses from reduced citrus production. A high-quality genome of D. citri is being manually annotated to provide accurate gene models to identify novel control targets and increase understanding of this pest. Here, we annotated 25 D. citri genes involved in glycolysis and gluconeogenesis, and seven in trehaloneogenesis. Comparative analysis showed that glycolysis genes in D. citri are highly conserved but copy numbers vary. Analysis of expression levels revealed upregulation of several enzymes in the glycolysis pathway in the thorax, consistent with the primary use of glucose by thoracic flight muscles. Manually annotating these core metabolic pathways provides accurate genomic foundation for developing gene-targeting therapeutics to control D. citri ., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

The hemipteran insect Diaphorina citri , or Asian citrus psyllid, is a vector for Candidatus Liberibacter asiaticus ( C Las), the bacterium causing citrus greening disease, or Huanglongbing (HLB). Millions of citrus trees have been destroyed, and every grove in Florida, USA, has been directly affected by this disease. In eukaryotes, vacuolar-type ATP synthase (V-ATPase) is an abundant heterodimeric enzyme that serves the cell with essential compartment acidification through the active processes that transport protons across the membrane. Fifteen putative V-ATPase genes in the D. citri genome were manually curated. Comparative genomic analysis revealed that D. citri V-ATPase subunits share domains and motifs with other insects, including the V-ATPase-A superfamily domain. Phylogenetic analysis separates D. citri V-ATPase subunits into expected clades with orthologous sequences. Annotation of the D. citri genome is a critical step towards developing directed pest management strategies to reduce the spread of HLB throughout the citrus industry., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2022.)

Genomic prediction (GP) offers great opportunities for accelerated genetic gains by optimizing the breeding pipeline. One of the key factors to be considered is how the training populations (TP) are composed in terms of genetic improvement, kinship/origin, and their impacts on GP. Hydrogen cyanide content (HCN) is a determinant trait to guide cassava's products usage and processing. This work aimed to achieve the following objectives: (i) evaluate the feasibility of using cross-country (CC) GP between germplasm's of Embrapa Mandioca e Fruticultura (Embrapa, Brazil) and The International Institute of Tropical Agriculture (IITA, Nigeria) for HCN; (ii) provide an assessment of population structure for the joint dataset; (iii) estimate the genetic parameters based on single nucleotide polymorphisms (SNPs) and a haplotype-approach. Datasets of HCN from Embrapa and IITA breeding programs were analyzed, separately and jointly, with 1,230, 590, and 1,820 clones, respectively. After quality control, ∼14K SNPs were used for GP. The genomic estimated breeding values (GEBVs) were predicted based on SNP effects from analyses with TP composed of the following: (i) Embrapa genotypic and phenotypic data, (ii) IITA genotypic and phenotypic data, and (iii) the joint datasets. Comparisons on GEBVs' estimation were made considering the hypothetical situation of not having the phenotypic characterization for a set of clones for a certain research institute/country and might need to use the markers' effects that were trained with data from other research institutes/country's germplasm to estimate their clones' GEBV. Fixation index (F ST ) among the genetic groups identified within the joint dataset ranged from 0.002 to 0.091. The joint dataset provided an improved accuracy (0.8-0.85) compared to the prediction accuracy of either germplasm's sources individually (0.51-0.67). CC GP proved to have potential use under the present study's scenario, the correlation between GEBVs predicted with TP from Embrapa and IITA was 0.55 for Embrapa's germplasm, whereas for IITA's it was 0.1. This seems to be among the first attempts to evaluate the CC GP in plants. As such, a lot of useful new information was provided on the subject, which can guide new research on this very important and emerging field., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Torres, Oliveira, Ogbonna, Bauchet, Mueller, Azevedo, Fonseca e Silva, Simiqueli and Resende.)

Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3'RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant-pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD., (© 2021. The Author(s).)

Insects have a segmented body plan that is established during embryogenesis when the anterior-posterior (A-P) axis is divided into repeated units by a cascade of gene expression. The cascade is initiated by protein gradients created by translation of maternally provided mRNAs, localized at the anterior and posterior poles of the embryo. Combinations of these proteins activate specific gap genes to divide the embryo into distinct regions along the anterior-posterior axis. Gap genes then activate pair-rule genes, which are usually expressed in parts of every other segment. The pair-rule genes, in turn, activate expression of segment polarity genes in a portion of each segment. The segmentation genes are generally conserved among insects, although there is considerable variation in how they are deployed. We annotated 25 segmentation gene homologs in the Asian citrus psyllid, Diaphorina citri . Most of the genes expected to be present in D. citri based on their phylogenetic distribution in other insects were identified and annotated. Two exceptions were eagle and invected , which are present in at least some hemipterans, but were not found in D. citri . Many of the segmentation pathway genes are likely to be essential for D. citri development, and thus they may be useful targets for gene-based pest control methods., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, which contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also be involved in bacterial defense. Here, we report the manual annotation of four CDA genes from the Asian citrus psyllid, Diaphorina citri , laying the groundwork for future study of these genes., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

The polysaccharide chitin is critical for the formation of many insect structures, including the exoskeleton, and is required for normal development. Here we report the annotation of three genes from the chitin synthesis pathway in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae), the vector of Huanglongbing (citrus greening disease). Most insects have two chitin synthase (CHS) genes but, like other hemipterans, D. citri has only one. In contrast, D. citri is unusual among insects in having two UDP-N-acetylglucosamine pyrophosphorylase (UAP) genes. One of the D. citri UAP genes is broadly expressed, while the other is expressed predominantly in males. Our work helps pave the way for potential utilization of these genes as pest control targets to reduce the spread of Huanglongbing., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

The Asian citrus psyllid, Diaphorina citri , is an insect vector that transmits Candidatus Liberibacter asiaticus, the causal agent of the Huanglongbing (HLB), or citrus greening disease. This disease has devastated Florida's citrus industry, and threatens California's industry as well as other citrus producing regions around the world. To find novel solutions to the disease, a better understanding of the vector is needed. The D. citri genome has been used to identify and characterize genes involved in Wnt signaling pathways. Wnt signaling is utilized for many important biological processes in metazoans, such as patterning and tissue generation. Curation based on RNA sequencing data and sequence homology confirms 24 Wnt signaling genes within the D. citri genome, including homologs for beta-catenin, Frizzled receptors, and seven Wnt-ligands. Through phylogenetic analysis, we classify D. citri Wnt ligands as Wg/Wnt1 , Wnt5 , Wnt6 , Wnt7 , Wnt10 , Wnt11 , and WntA . The D. citri version 3.0 genome with chromosomal length scaffolds reveals a conserved Wnt1-Wnt6-Wnt10 gene cluster with a gene configuration like that in Drosophila melanogaster . These findings provide greater insight into the evolutionary history of D. citri and Wnt signaling in this important hemipteran vector. Manual annotation was essential for identifying high quality gene models. These gene models can be used to develop molecular systems, such as CRISPR and RNAi, which target and control psyllid populations to manage the spread of HLB. Manual annotation of Wnt signaling pathways was done as part of a collaborative community annotation project., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

Huanglongbing (HLB), also known as citrus greening disease, is caused by the bacterium Candidatus Liberibacter asiaticus ( C Las). It is a serious threat to global citrus production. This bacterium is transmitted by the Asian citrus psyllid, Diaphorina citri (Hemiptera). There are no effective in planta treatments for C Las. Therefore, one strategy is to manage the psyllid population. Manual annotation of the D. citri genome can identify and characterize gene families that could be novel targets for psyllid control. The yellow gene family is an excellent target because yellow genes, which have roles in melanization, are linked to development and immunity. Combined analysis of the genome with RNA-seq datasets, sequence homology, and phylogenetic trees were used to identify and annotate nine yellow genes in the D. citri genome. Manual curation of genes in D. citri provided in-depth analysis of the yellow family among hemipteran insects and provides new targets for molecular control of this psyllid pest. Manual annotation was done as part of a collaborative Citrus Greening community annotation project., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content., (© The Author(s) 2020. Published by Oxford University Press.)

Key Message: Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Lasiodiplodia theobromae is a fungal pathogen associated with perennial tropical fruit plants worldwide. In citrus, L. theobromae causes stem-end rot (Diplodia stem-end rot), a damaging postharvest disease that is aggravated when trees are also infected with the citrus greening bacteria ' Candidatus Liberibacter asiaticus'. Due to the latent infection of L. theobromae during the preharvest stage, it becomes difficult to control the disease by chemical or physical treatment. In the current study, we sequenced and assembled strain CITRA15, the first genome of L. theobromae obtained from diseased Citrus paradise 'Flame' grapefruit in Florida, and thereby provided a genomic resource for future research on diagnostics, and postharvest and preharvest disease management of citrus and other fruit crops.

Background: Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency., Results: This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population., Conclusions: The availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.

Manihot esculenta (cassava) is a root crop originating from South America that is a major staple in the tropics, including in marginal environments. This study focused on South American and African germplasm and investigated the genetic architecture of hydrogen cyanide (HCN), a major component of root quality. HCN, representing total cyanogenic glucosides, is a plant defense component against herbivory but is also toxic for human consumption. We genotyped 3354 landraces and modern breeding lines originating from 26 Brazilian states and 1389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high-density genotyping using genotyping by sequencing. We performed genome-wide association mapping to characterize the genetic architecture and gene mapping of HCN. Field experiments revealed strong broad- and narrow-sense trait heritability (0.82 and 0.41, respectively). Two major loci were identified, encoding for an ATPase and a MATE protein, and contributing up to 7 and 30% of the HCN concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for the domestication of sweet and bitter cassava. Fine genomic characterization revealed: (i) the major role played by vacuolar transporters in regulating HCN content; (ii) the co-domestication of sweet and bitter cassava major alleles are dependent upon geographical zone; and (iii) the major loci allele for high HCN in M. esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together, these findings expand our insights into cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants., (© 2020 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

Modern breeding programs routinely use genome-wide information for selecting individuals to advance. The large volumes of genotypic information required present a challenge for data storage and query efficiency. Major use cases require genotyping data to be linked with trait phenotyping data. In contrast to phenotyping data that are often stored in relational database schemas, next-generation genotyping data are traditionally stored in non-relational storage systems due to their extremely large scope. This study presents a novel data model implemented in Breedbase (https://breedbase.org/) for uniting relational phenotyping data and non-relational genotyping data within the open-source PostgreSQL database engine. Breedbase is an open-source, web-database designed to manage all of a breeder's informatics needs: management of field experiments, phenotypic and genotypic data collection and storage, and statistical analyses. The genotyping data is stored in a PostgreSQL data-type known as binary JavaScript Object Notation (JSONb), where the JSON structures closely follow the Variant Call Format (VCF) data model. The Breedbase genotyping data model can handle different ploidy levels, structural variants, and any genotype encoded in VCF. JSONb is both compressed and indexed, resulting in a space and time efficient system. Furthermore, file caching maximizes data retrieval performance. Integration of all breeding data within the Chado database schema retains referential integrity that may be lost when genotyping and phenotyping data are stored in separate systems. Benchmarking demonstrates that the system is fast enough for computation of a genomic relationship matrix (GRM) and genome wide association study (GWAS) for datasets involving 1,325 diploid Zea mays, 314 triploid Musa acuminata, and 924 diploid Manihot esculenta samples genotyped with 955,690, 142,119, and 287,952 genotype-by-sequencing (GBS) markers, respectively., Competing Interests: The authors have declared that no competing interests exist.

Huanglongbing (HLB) is a deadly, incurable citrus disease putatively caused by the unculturable bacterium, 'Candidatus Liberibacter asiaticus' (CLas), and transmitted by Diaphorina citri. Prior studies suggest D. citri transmits CLas in a circulative and propagative manner; however, the precise interactions necessary for CLas transmission remain unknown, and the impact of insect sex on D. citri-CLas interactions is poorly understood despite reports of sex-dependent susceptibilities to CLas. We analyzed the transcriptome, proteome, metabolome, and microbiome of male and female adult D. citri reared on healthy or CLas-infected Citrus medica to determine shared and sex-specific responses of D. citri and its endosymbionts to CLas exposure. More sex-specific than shared D. citri responses to CLas were observed, despite there being no difference between males and females in CLas density or relative abundance. CLas exposure altered the abundance of proteins involved in immunity and cellular and oxidative stress in a sex-dependent manner. CLas exposure impacted cuticular proteins and enzymes involved in chitin degradation, as well as energy metabolism and abundance of the endosymbiont 'Candidatus Profftella armatura' in both sexes similarly. Notably, diaphorin, a toxic Profftella-derived metabolite, was more abundant in both sexes with CLas exposure. The responses reported here resulted from a combination of CLas colonization of D. citri as well as the effect of CLas infection on C. medica. Elucidating these impacts on D. citri and their endosymbionts contributes to our understanding of the HLB pathosystem and identifies the responses potentially critical to limiting or promoting CLas acquisition and propagation in both sexes., Competing Interests: The authors have declared that no competing interests exist.

Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams., Competing Interests: The authors declare no competing interests., (© 2020.)

Capsicum annuum is one of the most important horticultural crops worldwide. Anthracnose disease (Colletotrichum spp.) is a major constraint for chili production, causing substantial losses. Capsidiol is a sesquiterpene phytoalexin present in pepper fruits that can enhance plant resistance. The genetic mechanisms involved in capisidiol biosynthesis are still poorly understood. In this study, a 3' RNA sequencing approach was used to develop the transcriptional profile dataset of C. annuum genes in unripe (UF) and ripe fruits (RF) in response to C. scovillei infection. Results showed 4,845 upregulated and 4,720 downregulated genes in UF, and 2,560 upregulated and 1,762 downregulated genes in RF under fungus inoculation. Four capsidiol-related genes were selected for RT-qPCR analysis, two 5-epi-aristolochene synthase (CA12g05030, CA02g09520) and two 5-epi-aristolochene-1,3-dihydroxylase genes (CA12g05070, CA01g05990). CA12g05030 and CA01g05990 genes showed an early response to fungus infection in RF (24 h post-inoculation-HPI), being 68-fold and 53-fold more expressed at 96 HPI, respectively. In UF, all genes showed a late response, especially CA12g05030, which was 700-fold more expressed at 96 HPI compared to control plants. We are proving here the first high-throughput expression dataset of pepper fruits in response to anthracnose disease in order to contribute for future pepper breeding programs.

Presymptomatic detection of citrus trees infected with Candidatus Liberibacter asiaticus ( C Las), the bacterial pathogen associated with Huanglongbing (HLB; citrus greening disease), is critical to controlling the spread of the disease. To test whether infected citrus trees produce systemic signals that may be used for indirect disease detection, lemon ( Citrus limon ) plants were graft-inoculated with either C Las-infected or control ( C Las-) budwood, and leaf samples were longitudinally collected over 46 weeks and analyzed for plant changes associated with C Las infection. RNA, protein, and metabolite samples extracted from leaves were analyzed using RNA-Seq, mass spectrometry, and 1 H NMR spectroscopy, respectively. Significant differences in specific transcripts, proteins, and metabolites were observed between C Las-infected and control plants as early as 2 weeks post graft (wpg). The most dramatic differences between the transcriptome and proteome of C Las-infected and control plants were observed at 10 wpg, including coordinated increases in transcripts and proteins of citrus orthologs of known plant defense genes. This integrated approach to quantifying plant molecular changes in leaves of C Las-infected plants supports the development of diagnostic technology for presymptomatic or early disease detection as part of efforts to control the spread of HLB into uninfected citrus groves.

Cassava is an important staple crop in sub-Saharan Africa, due to its high productivity even on nutrient poor soils. The metabolic characteristics underlying this high productivity are poorly understood including the mode of photosynthesis, reasons for the high rate of photosynthesis, the extent of source/sink limitation, the impact of environment, and the extent of variation between cultivars. Six commercial African cassava cultivars were grown in a greenhouse in Erlangen, Germany, and in the field in Ibadan, Nigeria. Source leaves, sink leaves, stems and storage roots were harvested during storage root bulking and analyzed for sugars, organic acids, amino acids, phosphorylated intermediates, minerals, starch, protein, activities of enzymes in central metabolism and yield traits. High ratios of RuBisCO:phosphoenolpyruvate carboxylase activity support a C 3 mode of photosynthesis. The high rate of photosynthesis is likely to be attributed to high activities of enzymes in the Calvin-Benson cycle and pathways for sucrose and starch synthesis. Nevertheless, source limitation is indicated because root yield traits correlated with metabolic traits in leaves rather than in the stem or storage roots. This situation was especially so in greenhouse-grown plants, where irradiance will have been low. In the field, plants produced more storage roots. This was associated with higher AGPase activity and lower sucrose in the roots, indicating that feedforward loops enhanced sink capacity in the high light and low nitrogen environment in the field. Overall, these results indicated that carbon assimilation rate, the K battery, root starch synthesis, trehalose, and chlorogenic acid accumulation are potential target traits for genetic improvement., (© 2020 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

A collection of 163 accessions, including Solanum pimpinellifolium , Solanum lycopersicum var. cerasiforme and Solanum lycopersicum var. lycopersicum , was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication: Andean regions of Peru and Ecuador and Mesoamerica. The collection is enriched with S. lycopersicum var. cerasiforme from the Amazonian region that has not been analyzed previously nor used extensively. The collection has been morphologically characterized showing diversity for fruit, flower and vegetative traits. Their genomes were sequenced in the Varitome project and are publicly available (solgenomics.net/projects/varitome). The identified SNPs have been annotated with respect to their impact and a total number of 37,974 out of 19,364,146 SNPs have been described as high impact by the SnpEeff analysis. GWAS has shown associations for different traits, demonstrating the potential of this collection for this kind of analysis. We have not only identified known QTLs and genes, but also new regions associated with traits such as fruit color, number of flowers per inflorescence or inflorescence architecture. To speed up and facilitate the use of this information, F2 populations were constructed by crossing the whole collection with three different parents. This F2 collection is useful for testing SNPs identified by GWAs, selection sweeps or any other candidate gene. All data is available on Solanaceae Genomics Network and the accession and F2 seeds are freely available at COMAV and at TGRC genebanks. All these resources together make this collection a good candidate for genetic studies., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest., (© The Author(s) 2020.)

Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a phylogeny from 9868 orthologous genes, revealing several geographic clades but also high levels of gene discordance. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related, geographically co-occurring species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on each defense. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions., Competing Interests: TZ, SS, AP, MM, HA, MM, TY, CH, PK, ME, GP, JG, FP, CM, JP, LM, GJ No competing interests declared, (© 2020, Züst et al.)