Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism-an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information.     

Comparison between a coffee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coffee genome and the ancestral Arabidopsis genome

The Arabidopsis thaliana genome sequence provides a catalogue of reference genes that can be used for comparative analysis of other species thereby facilitating map-based cloning in economically important crops. We made use of a coffee bacterial artificial chromosome (BAC) contig linked to the S_H3 leaf rust resistance gene to assess microsynteny between coffee (Coffea arabica L.) and Arabidopsis. Microsynteny was revealed and the matching counterparts to C. arabica contigs were seen to be scattered throughout four different syntenic segments of Arabidopsis on chromosomes (Ath) I, III, IV and V. Coffee BAC filter hybridizations were performed using coffee putative conserved orthologous sequences to Arabidopsis predicted genes located on the different Arabidopsis syntenic regions. The coffee BAC contig related to the S_H3 region was successfully consolidated and later on validated by fingerprinting. Furthermore, the anchoring markers appeared in same order on the coffee BAC contigs and in all Arabidopsis segments with the exception of a single inversion on AtIII and AtIV Arabidopsis segments. However, the S_H3 coffee region appears to be closer to the ancestral genome segment (before the divergence of Arabidopsis and coffee) than any of the duplicated counterparts in the present-day Arabidopsis genome. The genome duplication events at the origin of its Arabidopsis counterparts occurred most probably after the separation (i.e. 94 million years ago) of Euasterid (Coffee) and Eurosid (Arabidopsis).     

The Importance of Ants and High-Shade Management to Coffee Pollination and Fruit Weight in Chiapas, Mexico

Recent reports show importance of pollinators to coffee and importance of ants as pollinators or floral protectors in many systems. Arthropod and pollinator diversity, however, declines with management intensification of coffee (Coffea arabica) agroecosystems. We investigated influences of both flying pollinators and ants on coffee fruit set and fruit weight in one high-shade (high-biodiversity) and one low-shade (low-biodiversity) coffee farm in Chiapas, Mexico through exclusion experiments. Contradictory to previous reports, flying pollinators alone did not affect coffee fruit set or fruit weight. Individual fruit weights, however, were higher on branches with both ants and flying pollinators (1.78 g ± 0.312 (SE)) compared to branches without ants (1.03 ± 0.029) or branches without ants or flying pollinators (1.05 ± 0.049), but only in the high-shade site. Although the mechanisms producing higher fruit weights are unknown, we discuss how ants or ant-flying pollinator interactions under high-shade coffee management may contribute to increased fruit weight and the implications of high-shade management for both sustainable coffee production and biodiversity conservation.     

Boron translocation in coffee trees

Boron deficiency in coffee trees (Coffea arabica) is widespread, however, responses to B fertilizer have been erratic, depending on the year, method, and time of application. A better understanding of B uptake, distribution, and remobilization within the plant is important in developing a rational fertilization program. Field and greenhouse experiments were conducted to study B distribution and remobilization in coffee trees. Boron was provided either in the nutrient solution or sprayed on the leaves of trees grown under adequate or transient B deficiency. There was clear evidence for B translocation via symplast (remobilization) to coffee grains, even in well-nourished plants. When ¹⁰B was present in the nutrient solution during most part of fruit filling, from 33 to 40% of the B found in coffee fruits was absorbed during this period, depending on the timing and duration of the B deficiency treatment. In the field, when B was sprayed once on the leaves, around 4% of the fruit B was derived from the foliar fertilizer. Boron remobilization within coffee trees is limited in well nourished plants, but it can be significant during periods of temporary B deficiency in plants otherwise well nourished with B. The implications of these findings for B fertilization practice, are discussed.     

Interaction of PvALF and VP1 B3 domains with the β-phaseolin promoter

Caffeine (1,3,7-trimethylxanthine) is derived from xanthosine through three successive transfers of methyl groups and a single ribose removal in coffee plants. The methyl group transfer is catalyzed by N-zmethyltransferases, xanthosine methyltransferase (XMT), 7-methylxanthine methyltransferase (MXMT) and 3,7-dimethylxanthine methyltransferase (DXMT). We previously cloned three genes encoding each of these N-methyltransferases from coffee plants, and reconstituted the final sequence of the caffeine synthetic pathway in vitro. In the present study, we simultaneously expressed these coffee genes in tobacco plants (Nicotiana tabacum), using a multiple-gene transfer method, and confirmed successful caffeine production up to 5 μg g⁻¹ fresh weight in leaves of the resulting transgenic plants. Their effects on feeding behavior of tobacco cutworms (Spodoptera litura), which damage a wide range of crops, were then examined. Leaf disc choice test showed that caterpillars selectively fed on the wild-type control materials, or positively avoided the transgenic materials. The results suggest a novel approach to confer self-defense by producing caffeine in planta. A second generation of transgenic crops containing caffeine may save labor and agricultural costs and also mitigate the environmental load of pesticides in future.     

The biology of Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) under field conditions

The coffee berry borer (CBB) Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae) was accidentally introduced into México in 1978, and rapidly became the main pest of coffee. As an exotic pest, its management has been mainly based on biological control methods through the introduction of parasitoids from Africa. In this context, at the beginning of the present decade, the parasitoid Phymastichus coffea LaSalle (Hymenoptera: Eulophidae) was imported to Mexico. Since then, several studies have been carried out as part of the post introduction evaluation of this parasitoid. In this paper, information concerning the parasitism and life-cycle of P. coffea in coffee farms is presented with the objective of providing information that elucidates its role as a biological control agent. P. coffea showed highly significant preferences for allocation of two eggs per host, usually one female and one male. Both offspring are able to develop and reach the adult stage successfully. Lifespan of adults is 2–3 days only. The degree of parasitism by P. coffea was more than 95% at the three altitudes tested, when releases consisted of a ratio of 10 CBB:1 parasitoid. The median survivorship of CBB parasitized by this wasp was 13, 15 and 19 days at the low, medium and high altitude coffee zones, respectively. The parasitism by P. coffea was higher when parasitoid releases were carried out simultaneously with the CBB, and decreased with the time between host and parasitoid releases. We showed that using P. coffea at a density of 1 parasitoid per 10 hosts resulted in a 3- to 5.6-fold decrease in CBB damage to the coffee seeds when compared to the control. The importance and value of these results are discussed in terms of the use of P. coffea as a biological control agent of the CBB in Latin America.     

Coffee pulp koji of Aspergillus sojae as stable immobilized catalyst of chlorogenate hydrolase

Chlorogenate hydrolase (EC 3.1.1.42, CHase) was highly induced in mycelia of Aspergillus sojae AKU 3312 grown in Czapek medium containing either instant coffee powder or coffee pulp as inducer. No CHase formation was observed in the mycelia when cultivated without the inducer. CHase was purified readily from CHase-induced mycelia to high homogeneity, and the purified CHase revealed the molecular weight of 180,000 consisting of two identical subunits of 88 kDa. Equimolar quinate (QA) and caffeate (CA) were confirmed on hydrolysis of chlorogenate (CGA). The purified CHase was only useful for a laboratory scale hydrolysis of CGA. For practical QA and CA production using scaled up hydrolysis of vegetable extracts of natural CGA resources, the enzyme activity of purified CHase decreased and denatured irreversibly. Preparation of coffee pulp koji and its application to QA and CA production were proposed instead of purified CHase. When coffee pulp koji was heated at 60°C for 30 min, CHase survived without any appreciable loss of enzyme activity while vegetative mycelial growth and spore germination were terminated. The heated coffee pulp koji thus prepared was effective itself as stable immobilized catalyst of CHase for QA and CA production from vegetable CGA resources such as coffee powders, coffee pulp, and others.     

Microclimatic changes and the indirect loss of ant diversity in a tropical agroecosystem

Recent changes in the coffee agroecosystem of Costa Rica were used to study the mechanism of biodiversity loss in transforming agroecosystems, focusing on the ground-foraging ant community. Coffee farms are being transformed from vegetationally diverse shaded agroforestry systems to unshaded coffee monocultures. We tested the hypothesis that the high-light environment and lack of leaf litter cover in the unshaded system are the determinants of the differences in ground-foraging ant diversity. Four treatments were established within the light gaps of a shaded plantation: shade, leaf litter, shade plus leaf litter, and a control (no shade or leaf litter added). Ants were sampled using tuna fish baits and light and temperature were measured. Shade and leaf litter had a significant effect on the ant fauna but probably for indirect reasons having to do with species interactions. In both shade treatments, Solenopsis geminata, the tropical fire ant, decreased significantly while the other species increased. The possibility that the physical factor changes the nature of competitive interactions between the most abundant species is discussed.     

Where to sample? Ecological implications of sampling strata in determining abundance and impact of natural enemies of the coffee berry borer,Hypothenemus hampei

Several parasitoids of African origin have been introduced to coffee producing areas of the Americas and Asia as biological control agents of the coffee berry borer (CBB) Hypothenemus hampei (Coleoptera: Curculionidae). These parasitoids have become established in the field but their effect on the CBB has been limited. A two-year field study in Western Kenya has found Prorops nasuta (Hymenoptera: Bethylidae) to be the predominant parasitoid emerging from CBB-infested coffee berries collected on coffee trees or from the ground. P. nasuta comprises more than 75% of the total natural enemies collected. The density of P. nasuta was 90% higher in the berries collected from the ground than from the trees. Its hyperparasitoid, Aphanogmus sp. (Hymenoptera: Ceraphronidae), also emerged from both type of berries. Across the two seasons, the average P. nasuta density per berry was 18–35 times higher than that of Aphanogmus sp. Throughout the two years sampled, significantly higher numbers of P. nasuta and Aphanogmus sp. occurred between February and March, which coincides with the beginning of the rainy season. Higher numbers of live CBB females were recorded in berries collected from the trees. Nevertheless, mortality of adult CBB was considerably higher from January to March and started to decrease from April onwards. The possibly negative effects of cultural control practices in Latin America which include the removal of berries fallen to the ground on biological control of CBB are discussed, and the use of screened collection devices for these berries which would permit the release of parasitoids but prevent escape of the pest is proposed.     

Epicatechin and catechin may prevent coffee berry disease by inhibition of appressorial melanization of Colletotrichum kahawae

Colletotrichum kahawae is the causal agent of coffee berry disease. Appressorial melanization is essential for the fungal penetration of plant cuticle. Epicatechin is abundant in green coffee berry pericarp. Inoculation of C. kahawae conidial suspension containing 1.2 mg epicatechin or catechin/ml did not affect conidial germination or appressorial formation but appressorial melanization was completely inhibited and infection by the treated conidia was less than 30% of the untreated control. Epicatechin and catechin may, therefore, prevent coffee berry disease by inhibition of the appressorial melanization of C. kahawae.     

Life history studies of <Emphasis Type="Italic">Prorops nasuta</Emphasis>, a parasitoid of the coffee berry borer

Life history studies were conducted in the laboratory on the African parasitoid Prorops nasuta Waterston (Hymenoptera: Bethylidae), a parasitoid of the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae). The female wasp enters an infested coffee berry, kills the adult borer and seals the entrance of the berry with the body of the borer, impeding the entry of other organisms into the berry. The preoviposition period ranges from 3 to 14 days (mean 5.42 ± 0.37 SE). During this time females feed on the immature stages and paralyse fully grown larvae and pupae of the CBB. P. nasuta is an idiobiont solitary ectoparasitoid. Eggs are laid externally on the last instar larvae and pupae. Mean development time (egg to adult) for males and females was 27.7 (±0.37 SE) and 30 (±0.12 SE) days, respectively. Median survival for wasps fed on final instar CBB larvae was 27.7 days, significantly longer than any other treatment, while for females without food it was 2.5 days. In culture, females produced an average of 4.3 (±0.39 SE) progeny during their lifetimes. Adults began emerging at 30.6 days (±0.28 SE) after cultures were started and peak production was reached at 36 days, declining thereafter. Males normally emerged from coffee beans 2–3 days before females. Males usually emerged from 07:00 to 09:00h and females from 10:00 to 14:00 h. The culture sex ratio (proportion of males) was 0.21. Virgin females produced only male offspring.     

Advances in coffee tissue culture and its practical applications

Genetic improvement of coffee, an important commercial crop, through classical breeding is slow and cumbersome. Biotechnology offers alternative strategies for generating new and improved coffee varieties, including those resistances to environmental extremes, pests, and diseases, low in caffeine, and with uniform fruit maturation. Large improvements in somatic embryogenesis, development of haploids, and scale-up of micropropagation have been accomplished in the last 5 yr. The recent identification of expressed sequence tags (EST) that are differentially expressed during the infestation of coffee plants by coffee leaf miners and the isolation and cloning of the promoter for the N-methyltransferase gene associated with caffeine production open up the possibility of producing varieties of coffee with new traits. This review provides a summary of in vitro biological advances and directions as to how they could be applied to improve the production and quality of coffee.     

Allantoin has a limited role as nitrogen source in cultured coffee cells

In plants the ureides allantoin (ALN) and allantoic acid (ALA) are formed in purine metabolism, and in some legumes both compounds play an important role as nitrogen (N) sources. In coffee plants, ALN and ALA are catabolites of caffeine degradation. Caffeine is found throughout the coffee plant and in some parts this alkaloid can accumulate up to 4% dry basis. Therefore, caffeine degradation via ureides may make an important contribution to N metabolism of the plant. Using coffee cell suspension as a model we investigated the contribution of ALN as a source of N in coffee. ALN was incorporated in the liquid medium and after 20 d of cultivation, cell mass, NO(3), NH(4), amino acids, soluble proteins, ALN and caffeine were determined in the cells. The activity of glutamine synthetase was also studied. The results showed that despite being taken up by cells ALN does not contribute significantly as a source of N in coffee cells. Compared with mineral N sources, cells grown with ALN-N accumulated much less mass. The inclusion of ALN in the medium caused significant alterations in the content of some N compounds indicating a stress condition.     

Robusta coffee beans post-harvest microflora: Lactobacillus plantarum sp. as potential antagonist of Aspergillus carbonarius

Coffee contamination by ochratoxigenic fungi affects both coffee quality as well as coffee price with harmful consequences on the economy of the coffee exporting countries for whom which is their main source of income. Fungal strains were isolated from coffee beans and identified as black Aspergilli. Ochratoxigenic moulds like Aspergillus carbonarius were screened and selected for detailed studies. Also lactic acid bacteria (LAB) were isolated from silage coffee pulp and their antifungal activity was tested on dual-culture agar plate. Ten of the isolated LAB demonstrated antifungal effect against A. carbonarius. API 50 CH and APIZYM were used to perform phenotypic identification. 16S rDNA sequencing was made to confirm the results.     

Insect natural enemies of coffee green scales [Hemiptera: Coccidae] in Kenya and their potential for biological control ofCoccus celatus andC. viridis in Papua New Guinea

Coffee green scales,Coccus celatus De Lotto andC. viridis (Green), are major pests of coffee in Papua New Guinea (PNG). Surveys for insect natural enemies of coffee green scales were conducted in Kenya to find species suitable for introduction to PNG. Natural enemy communities in Kenya were found to be diverse, particularly those located in the central highlands where 3 primary parasitoids,Metaphycus stanleyi Compere,M. baruensis Noyes andDiversinervus stramineus Compere (Encyrtidae), were dominant onC. celatus andC. alpinus De Lotto. It is suggested that these 3 parasitoids may be potential biological control agents forC. celatus. Several insect predators were found associated withC. celatus in the central highlands but most were only common in ant-free scale populations. An aphelinid primary parasitoid,Coccophagus rusti Compere, was the only natural enemy ofC. viridis located. This species, however, could be of potential as a biological control agent, especially in view of its previous use in biological control against soft scales.      

Tropical rain forest fragmentation and wild populations of primates at Los Tuxtlas,Mexico

In view of the extensive destruction, fragmentation, and conversion of primate habitats to anthropogenic vegetation, information on Neotropical primate ability to use a landscape consisting of forest fragments and agricultural habitats is necessary to understand the ecological flexibility of the species involved and it is of relevance to the design of conservation scenarios at the landscape level. We censused howlers and spider monkeys in 126 forest fragments and in 44 agricultural sites at Los Tuxtlas, southern Veracruz, Mexico, and used the IDRISI Geographic Information System to assess the extent of primate habitat remaining. We conducted economic surveys to assess the productivity of several systems of land management, including cattle ranching. Seventy- five percent of native habitat has been lost at Los Tuxtlas, 20% remains in the form of isolated fragments of vegetation, and only 5% consists of contiguous rain forest at high elevations (> 800 m). Howlers and spider monkeys were present in only 60 and 8% of the forest sites investigated, respectively, attesting to extensive local extinction. Populations of both species are small and found in a fragmented and isolated condition throughout the landscape. A large number of howlers were detected in artifactual habitats such as cacao, coffee and mixed (cacao and coffee) plantations shaded by rain forest trees. Residual rain forest vegetation along streams, rivers, and lakes facilitated the interfragment and interhabitat movement of howlers. Economic surveys showed that some of the agricultural habitats were more productive than cattle ranching. Conservation of spider monkeys requires large areas of contiguous forest, but only small areas are present at high elevations. Howlers are restricted to elevations < 800 m, where most of the forest has disappeared, but can apparently exist in a matrix of forest fragments, arboreal agricultural habitats, and pasture lands. Structural aspects of the vegetation and connectivity among habitat islands may be indispensable components of both landscape scenarios.     

Secondary metabolites of <Emphasis Type="Italic">Penicillium</Emphasis> fungi isolated from permafrost deposits as chemotaxonomic markers

Species identification of slow-growing fungi of the genus Penicillium isolated from ancient permafrost deposits was performed using micro- and macromorphological characteristics as well as the composition of secondary metabolites. The strains producing clavine ergot alkaloids fumigaclavines A and B and festuclavine were assigned to the species P. palitans Westling 1911, whereas the strains forming ochratoxins A and B were identified as P. verrucosum Dierckx 1901.     

Transgenic tobacco plants producing caffeine: a potential new strategy for insect pest control

Caffeine (1,3,7–trimethylxanthine) is one of the most widely used plant secondary metabolites, primarily as a stimulant and an ingredient in drugs. In nature, caffeine is believed to function in chemical defense, acting as an antiherbivory and allelopathic agent, and therefore it might be employed to protect agriculturally important crop plants. In coffee plants, caffeine is synthesized from the precursor xanthosine in four steps, three N-methylations and removal of ribose. We had previously isolated genes encoding three distinct N-methyltransferases, and we demonstrated production of recombinant enzymes that yielded caffeine in in vitro reconstitution experiments. When these caffeine biosynthetic pathway genes were simultaneously expressed in tobacco plants (Nicotiana tabacum), caffeine was successfully produced up to 5 μg/g fresh weight in leaves. The leaves were unpalatable to tobacco cutworms (Spodoptera litura). This repellent action appeared to be more widely␣applicable to lepidopteran caterpillars as observed with small white (Pieris rapae) fed on Chinese cabbages that had been top-treated with caffeine. Our recent results suggest a novel approach to strengthen anti-herbivore traits by producing caffeine in crop plants.     

Seasonal changes in photoprotective mechanisms of leaves from shaded and unshaded field-grown coffee (<Emphasis Type="Italic">Coffea arabica</Emphasis> L.) trees

Coffee is native to shady environments, but often grows and yields better without shade. Thus, it may be reasoned that coffee leaves should display enough plasticity to acclimate themselves to contrasting light environments. However, little is known about mechanisms associated with such plasticity in coffee. This work aimed, therefore, to explore differences in leaf photoprotective mechanisms. Plants were grown in the field and received either 48 or 100% natural light. Evaluations were made using outer leaves from the sun-facing sides of the coffee hedgerow in Viçosa (Brazil) in August and October, when growth and photosynthetic rates are expected to be minimal and maximal, respectively, and in December, when temporary depressions in those variables are common. Regardless of light treatments, coffee leaves showed: (1) very low photosynthetic rates (generally below 2.5 μmol m^?2 s^?1), (2) chronic photoinhibition in August (dry, cool season) that was accompanied by strong loss of pigment concentration, and (3) discrete, dynamic photoinhibition in October and December (rainy, warm season). Compared with shaded leaves, sunlit leaves generally exhibited lower pigment concentration, lower quantum yield of electron transport, steeper inclinations and similar electron transport rate. Total ascorbate pool tended to be larger in sunlit than in shaded leaves (but with similar redox state), whereas activities of key antioxidant enzymes, as well as malondialdehyde accumulation and electrolyte leakage, were similar between those leaf types. As a whole, the photosynthetic apparatus of the coffee tree showed a low phenotypic plasticity to varying irradiance.