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Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. While attempting to isolate Ceratobasidium theobromae, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were Lasiodiplodia spp. Sequence-based identification of 52 putative isolates of L. theobromae indicated that diverse species of Lasiodiplodia were associated with cacao in the studied areas, and the isolates showed variation in aggressiveness when assayed using cacao leaf discs. The present study reports a 43.75 Mb de novo assembled genome of an isolate of L. theobromae from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to L. theobromae, when compared with other closely related Botryosphaeriaceae. Transcriptome analysis revealed that 11 860 predicted genes were transcriptionally active and 1255 were more highly expressed in planta compared with cultured mycelia. The predicted genes differentially expressed during infection were mainly those involved in carbohydrate, pectin, and lignin catabolism, cytochrome P450, necrosis-inducing proteins, and putative effectors. These findings significantly expand our knowledge of the genome of L. theobromae and the genes involved in virulence and pathogenicity. Keywords: cacao, Lasiodiplodia, genome, transcriptome, effectors. Le Lasiodiplodia theobramae (Pat.) Griffon & Maubl., un membre de la famille des Botryosphaeriaceae, est en train de devenir une menace importante chez plusieurs cultures et especes ligneuses dans plusieurs regions du monde, incluant les regions productrices de cacaoyer. En tentant d'isoler le Ceratobasidium theobromae, l'agent causal du deperissement avec necrose vasculaire (VSD), a partir de tiges symptomatiques, 74 % des champignons isoles appartenaient aux Lasiodiplodia spp. Une identification moleculaire de 52 isolats putatifs du Lasiodiplodia a permis de montrer que diverses especes de Lasiodiplodia etaient associees au cacaoyer dans les regions etudiees et que ces isolats montraient une agressivite variable lorsque celle-ci etait mesuree sur des disques foliaires. La presente etude rapporte un genome de 43,75 Mb assemble de novo a partir d'un isolat L. theobromae du cacaoyer. Une prediction de genes ab initio a produit 13 061 genes codant pour des proteines, dont 2862 etaient uniques au L. theobromae par rapport a d'autres Botryosphaeriaceae. Une analyse transcriptomique a revele que 11 860 des genes predits etaient transcrits et que 1255 de ceux-ci etaient plus fortement exprimes in planta que chez le mycelium en culture. Les genes predits qui etaient exprimes de maniere differentielle au cours de l'infection etaient principalement ceux impliques dans le catabolisme des hydrates de carbone, de la pectine et de la lignine, ainsi que des cytochromes P450, des proteines induisant la necrose et des effecteurs putatifs. Ces resultats accroissent significativement nos connaissances sur le genome ainsi que les genes du L. theobromae que sont impliques dans la virulence et la pathogenicite. [Traduit par la Redaction] Mots-cles : cacaoyer, Lasiodiplodia, genome, transcriptome, effecteurs., Introduction Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is often considered a latent plant pathogen attacking more than 500 plant species in the tropics and [...]

Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya 'Booth' cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity analysis. Phylogenetic analysis supports that eudicots and magnoliids are more closely related to each other than to monocots. Moreover, the Magnoliales was found to be more closely related to the Laurales than the Piperales. Genome comparison revealed that the 'Booth' cultivar has 200 Mb less repeats than the Spanish cultivar 'Fino de Jete', despite their highly similar (>99%) genome sequence identity and collinearity. These two cultivars were diverged during the early Pleistocene (1.93 Mya), which suggests a different origin and domestication of the cherimoya. Terpene/terpenoid metabolism functions were found to be enriched in Magnoliales, while TNL (Toll/Interleukin-1-NBS-LRR) disease resistance gene has been lost in Magnoliales during evolution. We have also identified a gene cluster that is potentially responsible for the biosynthesis of acetogenins, a class of natural products found exclusively in Annonaceae. The cherimoya genome provides an invaluable resource for supporting characterization, conservation, and utilization of Annona genetic resources. [ABSTRACT FROM AUTHOR]

Tea is a steeped beverage made from the leaves of Camellia sinensis. Globally, this healthy, caffeine-containing drink is one of the most widely consumed beverages. At least 50 countries produce tea and most of the production information and tea research is derived from international sources. Here, we discuss information related to tea production, genetics, and chemistry as well as production issues that affect or are likely to affect emerging tea production and research in the United States. With this review, we relay current knowledge on tea production, threats to tea production, and solutions to production problems to inform this emerging market in the United States. [ABSTRACT FROM AUTHOR]

Population structure of the old Trinitario cacao (Theobroma cacao L.) in Trinidad was evaluated from the 35-microsatellite multilocus profile of 32 relict clones from abandoned cocoa estates in Trinidad (TRD) and 88 Imperial College selections (ICS) clones conserved in the International Cocoa Genebank, Trinidad. Ancestry was derived by comparison to 34 representative genotypes of Criollo, Central American, and Lower and Upper Amazon origin. The 154 individuals separated into four populations in this study, labeled Population 1--Upper Amazon; Population 2--Ecuadorian; Population 3--Lower Amazon; and Population 4--Trinitario. Over 90% of the individuals demonstrated 70 to 99% membership to their respective populations. The ICS and TRD clones formed a genetically homogenous group, 84% of which clustered in Population 4 with clones of pure Criollo descent. Another 10% clustered in Population 1 containing clones of Upper Amazon descent. The cacao population of Trinidad is genetically different from clones of Ecuadorian and Lower Amazon descent, Populations 2 and 3, respectively. The 10 most discriminating loci for each population were different as shown by polymorphism information content values for each of the 35 microsatellite loci. This is the first report to provide a strong genetic basis for the industry flavor distinction of Trinitario and Ecuadorian cacaos. These findings significantly impact germplasm fingerprinting and curatorship and maintenance of industry flavor classes while breeding for disease resistance in cacao.

Abstract Background The basidiomycete fungus Moniliophthora perniciosa is the causal agent of Witches' Broom Disease (WBD) in cacao (Theobroma cacao). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. M. perniciosa, together with the related species M. roreri, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9× coverage) of M. perniciosa was analyzed to evaluate the overall gene content of this phytopathogen. Results Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that M. perniciosa has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that M. perniciosa have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in M. perniciosa genome survey. Conclusion This genome survey gives an overview of the M. perniciosa genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the M. perniciosa/cacao pathosystem.