Consequences of stoichiometric error on nuclear DNA content evaluation in Coffea liberica var. dewevrei using DAPI and propidium iodide

The genome size of coffee trees (Coffea sp.) was assessed using flow cytometry. Nuclear DNA was stained with two dyes [4',6-diamino-2-phenylindole dihydrochloride hydrate (DAPI) and propidium iodide (PI)]. Fluorescence in coffee tree nuclei (C-PI or C-DAPI) was compared with that of the standard, petunia (P-PI or P-DAPI). If there is no stoichiometric error, then the ratio between fluorescence of the target nuclei and that of the standard nuclei (R-PI or R-DAPI) is expected to be proportional to the genome size. Between-tree differences in target : standard fluorescence ratios were noted in Coffea liberica var. dewevrei using propidium iodide and DAPI. For both dyes, between-tree differences were due to a lack of proportionality when comparing locations of the coffee peak and the petunia peak. Intraspecific genome size variations clearly cannot explain variations in the target : standard fluorescence ratio. The origin of the lack of proportionality between target and standard fluorescences differed for the two dyes. With propidium iodide, there was a regression line convergence point, and no between-tree differences were noted in this respect, whereas there was no such convergence with DAPI. An accurate estimate of genome size can thus be obtained with PI. Implications with respect to accessibility and binding mode are discussed.     

Trypanosomatids, Other Than Phytomonas spp., Isolated and Cultured from Fruit

Trypanosomatids were isolated from edible fruit. One of the isolates (from tangerine) presented a set of enzymes for the metabolism of arginine-ornithine similar to that of Leptomonas spp., and failed to be recognized by monoclonal antibodies specific for Phytomonas spp. The possibility that trypanosomatids other than Phytomonas spp. could infect fruit was further examined by inoculating tomatoes with species of Crithidia, Leptomonas and Herpetomonas. Some of these flagellates multiplied in tomatoes. Besides, house flies became infected with Crithidia sp. when fed on tomatoes experimentally inoculated with this flagellate. Therefore, isolation of a trypanosomatid from a plant should not constitute an absolute criterion for placing it in the genus Phytomonas.     

Growth of Phytomonas serpens in a Defined Medium; Nutritional Requirements

ABSTRACT. Three strains of Phytomonas serpens two from tomatoes, Lycopersicon esculentum one from the insect Phtia picta (Hemiptera, Coreidae), were cultivated in a chemically defined medium developed from a defined medium for cultivating insect flagellates. Besides organic growth factors required by other insect trypanosomatids this flagellate requires, serine and inositol. Glutamine stimulates growth, and, surprisingly, does not require heme.     

AFLP analysis of genetic diversity within and among Coffea arabica cultivars

Genetic diversity of Coffea arabica cultivars was estimated using amplified fragment length polymorphism (AFLP) markers. Sixty one Coffea accessions composed of six arabica cultivars, including Typica, Bourbon, Catimor, Catuai, Caturra and Mokka Hybrid, plus two diploid Coffea species, were analyzed with six EcoRI- MseI primer combinations. A total of 274 informative AFLP markers were generated and scored as binary data. These data were analyzed using cluster methods in the software package NTSYSpc. The differences among cultivars at the DNA level were small, with an average genetic similarity of 0.933. Most accessions within a cultivar formed a cluster, although deviant samples occurred in five of the six cultivars examined due to residual heterozygosity from ancestral materials. Among the six cultivars fingerprinted, the highest level of genetic diversity was found within the cultivar Catimor, with an average genetic similarity of 0.880. The lowest level was found within Caturra accessions, with an average genetic similarity of 0.993. Diversity between C. arabica and two other Coffea species, Coffea canephora and Coffea liberica, was also estimated with average genetic similarities of 0.540 and 0.413, respectively, suggesting that C. canephora is more closely related to C. arabica than is C. liberica. The genetic variation among arabica cultivars was similar to the variation within cultivars, and no cultivar-specific DNA marker was detected. Although arabica cultivars appear to have a narrow genetic base, our results show that sufficient polymorphism can be found among some arabica cultivars with a genetic similarity as low as 0.767 for genetic/QTL mapping and breeding. The assessment of genetic diversity among arabica cultivars provided the necessary information to estimate the potential for using marker-assisted breeding for coffee improvement.     

Trypanosomatidae: Phytomonas detection in plants and phytophagous insects by PCR amplification of a genus-specific sequence of the spliced leader gene

In this paper we describe a method for the detection of Phytomonas spp. from plants and phytophagous insects using the PCR technique by targeting a genus-specific sequence of the spliced leader (SL) gene. PCR amplification of DNA from 48 plant and insect isolates previously classified as Phytomonas by morphological, biochemical, and molecular criteria resulted in all cases in a 100-bp fragment that hybridized with the Phytomonas-specific spliced leader-derived probe SL3'. Moreover, this Phytomonas-specific PCR could also detect Phytomonas spp. in crude preparations of naturally infected plants and insects. This method shows no reaction with any other trypanosomatid genera or with plant and insect host DNA, revealing it to be able to detect Phytomonas spp. from fruit, latex, or phloem of various host plants as well as from salivary glands and digestive tubes of several species of insect hosts. Results demonstrated that SLPCR is a simple, fast, specific, and sensitive method that can be applied to the diagnosis of Phytomonas among cultured trypanosomatids and directly in plants and putative vector insects. Therefore, the method was shown to be a very specific and sensitive tool for diagnosis of Phytomonas without the need for isolation, culture, and DNA extraction of flagellates, a feature that is very convenient for practical and epidemiological purposes.     

Genetic mapping of a caffeoyl-coenzyme A 3-O-methyltransferase gene in coffee trees. Impact on chlorogenic acid content

Chlorogenic acids (CGA) are involved in the bitterness of coffee due to their decomposition in phenolic compounds during roasting. CGA mainly include caffeoyl-quinic acids (CQA), dicaffeoyl-quinic acids (diCQA) and feruloyl-quinic acids (FQA), while CQA and diCQA constitute CGA sensu stricto (CGA s.s.). In the two cultivated species Coffea canephora and Coffea arabica, CGA s.s. represents 88% and 95% of total CGA, respectively. Among all enzymes involved in CGA biosynthesis, caffeoyl-coenzyme A 3-O-methyltransferase (CCoAOMT) is not directly involved in the CGA s.s. pathway, but rather in an upstream branch leading to FQA through feruloyl-CoA. We describe how a partial cDNA corresponding to a CCoAOMT encoding gene was obtained and sequenced. Specific primers were designed and used for studying polymorphism and locating the corresponding gene on a genetic map obtained from an interspecific backcross between Coffea liberica var. Dewevrei and Coffea pseudozanguebariae. Offspring of this backcross were also evaluated for the chlorogenic acid content in their green beans. A 10% decrease was observed in backcross progenies that possess one C. pseudozanguebariae allele of the CCoAOMT gene. This suggests that CGA s.s. accumulation is dependent on the CCoAMT allele present and consequently on the activity of the encoded isoform, whereby CGA accumulation increases as the isoform activity decreases. Possible implications in coffee breeding are discussed.     

Inheritance of seed desiccation sensitivity in a coffee interspecific cross: evidence for polygenic determinism

The genetic determinism of seed desiccation sensitivity was studied using a cross between two coffee species exhibiting a large difference for this trait, Coffea pseudozanguebariae (tolerant) and C. liberica (sensitive). Throughout the whole study, seed desiccation tolerance was quantified both in terms of water content and water activity. Whatever the parameter used, the level of seed desiccation tolerance in F1 hybrids corresponded to that of the mid-parent, thus indicating an additive inheritance of seed desiccation tolerance at the F1 level. A broad variation was observed among hybrids backcrossed to C. liberica (BCs) for seed desiccation tolerance, independent of the parameter used to quantify it. This variation was continuous and BCs showed transgression in the direction of the most desiccation sensitive parent, indicating (i) that desiccation tolerance is a polygenic trait in coffee species, and (ii) that C. pseudozanguebariae does not present the most favourable alleles for all the genes involved in seed desiccation tolerance. No significant difference was observed between the two reciprocal backcrosses, F1xC. liberica and C. libericaxF1, for the level of desiccation tolerance of their seeds, showing the absence of a maternal effect on this trait. There was no significant effect of the number of seeds harvested from each BC on the level of desiccation tolerance of its seeds. Moreover, there was no significant correlation within BCs between seed size, seed viability, and water content before desiccation and desiccation tolerance.     

Life Cycle and Culturing of Phytomonas serpens (Gibbs), a Trypanosomatid Parasite of Tomatoes

Pure cultures of a trypanosomatid isolated from tomato fruits infected laboratory-raised tomatoes and nymphs of the hemipieran coreid Phthia picta . The flagellate could be transmitted back and forth from tomatoes to insects. Light and electron microscopy studies were done on culture, tomato and insect forms. Examination of enzymes of the ornithine-arginine metabolism revealed absence of arginase and presence of arginine deiminase and citrulline hydrolase. Monoclonal antibodies specific for Phytomonas spp. reacted positively with tomato and insect forms. Endonuclease digestion of the k-DNA of various Phytomonas spp. revealed a unique, distinctive pattern for the tomato flagellate. This flagellate thus seems to constitute a separate species of Phytomonas which we now call Phytomonas serpens (Gibbs).     

Canker and wilt of black locust (Robinia pseudoacacia L.) caused by Fusarium species

From the pathological material of black locust trees showing symptoms of wilting of the foliage or canker of the bark the following Fusarium species were isolated: Fusarium avenaceum (Fr.) Sacc., Fusarium lateritium Nees., Fusarium semitectum Berk. & Rav., Fusarium solani (Mart.) Sacc., Fusarium sulphureum Schlecht. (syn.: Fusarium sambucinum Fuckel f. 6 Wollenw.) The results of the provocation infections of one-year-old black locust seedlings showed that all of the species--except Fusarium solani--are able to cause considerable necrosis in living bark and phloem. Fusarium sulphureum had by far the highest pathogenecity among the tested species. Fusarium semitectum isolated from withered black locust tree also caused necrosis on significant bark area. In the course of the penetration assay Fusarium sulphureum and Fusarium avenaceum were the most successful, and these species can cause cankers on the stem and twigs of black locust without frost effect.     

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.).

Fluorescence in situ hybridization (FISH) was used to study the presence of alien chromatin in interspecific hybrids and one introgressed line (S.288) derived from crosses between the cultivated species Coffea arabica and the diploid relatives C. canephora and C. liberica. In situ hybridization using genomic DNA from C. canephora and C. arabica as probes showed elevated cross hybridization along the hybrid genome, confirming the weak differentiation between parental genomes. According to our genomic in situ hybridization (GISH) data, the observed genomic resemblance between the modern C. canephora genome (C) and the C. canephora-derived subgenome of C. arabica (Ca) appears rather considerable. Poor discrimination between C and Ca chromosomes supports the idea of low structural modifications of both genomes since the C. arabica speciation, at least in the frequency and distribution of repetitive sequences. GISH was also used to identify alien chromatin segments on chromosome spreads of a C. liberica-introgressed line of C. arabica. Further, use of GISH together with BAC-FISH analysis gave us additional valuable information about the physical localization of the C. liberica fragments carrying the SH3 factor involved in resistance to the coffee leaf rust. Overall, our results illustrate that FISH analysis is a complementary tool for molecular cytogenetic studies in coffee, providing rapid localization of either specific chromosomes or alien chromatin in introgressed genotypes derived from diploid species displaying substantial genomic differentiation from C. arabica.     

SSR cross-amplification and variation within coffee trees (Coffea spp.).

Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was -11% for PSE and -9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.     

Experimental Infection of Various Latex Plants of the Family Asclepiadaceae with Phytomonas elmassiani

SYNOPSIS. Trypanosomatid-free plants of the family Asclepiadaceae identified as Asclepias syriaca, A. curassavica, A. incarnata, Stephanotis floribunda, Seutera maritima, Amphistelma scoparia and plants of the family Euphorbiaceae identified as Euphorbia tirucalli, E. trigona , and Pedilanthus tithymaloides were exposed to the bite of the bug, Oncopeltus fasciatus , infected with Phytomonas elmassiani , a flagellate which occurs naturally in A. syriaca and O. fasciatus . Two weeks subsequent to exposure to laboratory-infected oncopeltids all the experimental Asclepiadaceae were infected. The mean length of the protozoa varied depending on the host plant. The flagellates in A. syriaca, A. curassavica , and A. incarnata were shorter than those in S. floribunda, S. maritima , and A. scoparia .
None of the Euphorbiaceae became infected.     

Functional aspects of secondary carotenoids in Haematococcus lacustris (Girod) Rostafinski (Volvocales). V. Influences on photomovement

Secondary carotenoids are suspected to modulate photomovement in Haematococcus lacustris [Girod] Rostafinski (Volvocales). To investigate the influence of these extrachloroplastic ketocarotenoids on phototactic and photophobic responses in the flagellate stage of the green alga, flagellate suspensions differing in the content of secondary carotenoids were grown from green and red aplanospores. Photo-orientation of these flagellates induced by unilateral irradiation was investigated using a computer-aided system for microscopic image analysis. Results were hypothetically summarized as follows: (1) Diminution of precision of the positive phototaxis was found in red flagellates. This might be due to cellular shading of the blue-light-sensitive photoreceptor by secondary carotenoids. (2) Red flagellates exhibited an increase in the photophobic response. This finding is discussed in relation to an adaptive increase of the photoreceptor sensitivity, thought to be a result of the higher optical density of the corresponding cell suspension in the blue wavelength region.     

具血型转换功能的咖啡α-半乳糖苷酶基因的克隆与表达

从大粒种咖啡(Coffea liberica)和中粒种咖啡(Coffea canephora)中分离克隆到了α-半乳糖苷酶（α-D-galactosidase）cDNA的开放阅读框架即编码区,分别记为Gal-D与Gal-Z,长度与已发表的小粒种咖啡cDNA编码序列相同均为1 089 bp,同源性与已发表的小粒种咖啡cDNA编码序列相比分别为98.7%和99.27%。 将克隆到的Gal-D与Gal-Z用巴斯德毕赤氏酵母Pichia pastoris表达载体pPICZαA（分泌甲醇诱导型）和pGAPZαA（分泌组成型）成功地构建了如下酵母表达载体：pPICZαA/Gal-Z,pPICZαA/Gal-D和pGAPZαA/Gal-D,并转入酵母宿主菌GS115进行了发酵表达研究。实验得出工程菌株pPICZαA/Gal-D / GS115的重组表达产物酶活最高可达48.22（U/mL）,对发酵产物进行了SDS-PAGE电泳,得到一条清晰的主条带。     

Arthropod biodiversity loss and the transformation of a tropical agro-ecosystem

The coffee (Coffea arabica) agro-ecosystem in the Central Valley of Costa Rica was formerly characterized by a high vegetational diversity. This complex system has been undergoing a major transformation to capital-intensive monocultural plantations where all shade trees are eliminated. In this study we examined the pattern of arthropod biodiversity loss associated with this transformation. Canopy arthropods were sampled in three coffee farms: a traditional plantation with many species of shade trees, a moderately shaded plantation with only Erythrina poeppigeana and coffee, and a coffee monoculture. An insecticidal fogging technique was used to sample both canopy and coffee arthropods. Data are presented on three major taxonomic groups: Coleoptera, non-formicid Hymenoptera, and Formicidae. Data demonstrate that the transformation of the coffee agro-ecosystem results in a significant loss of biological diversity of both canopy arthropods as well as arthropods living in coffee bushes. Percentage of species overlap was very small for all comparisons. Furthermore, species' richness on a per tree basis was found to be within the same order of magnitude as that reported for trees in tropical forests. If results presented here are generalizable, this means that conservation efforts to preserve biological diversity should also include traditional agro-ecosystems as conservation units.     

The role of actin, actomyosin and microtubules in defining cell shape during the differentiation of Naegleria amebae into flagellates

Differentiation of Naegleria amebae into flagellates was used to examine the interaction between actin, actomyosin and microtubules in defining cell shape. Amebae, which lack microtubules except during mitosis, differentiate into flagellates with a fixed shape and a complex microtubule cytoskeleton in 120 min. Based on earlier models of ameboid motility it has been suggested that actomyosin is quiescent in flagellates. This hypothesis was tested by following changes in the cytoskeleton using three-dimensional reconstructions prepared by confocal microscopy of individual cells stained with antibodies against actin and tubulin as well as with phalloidin and DNase I. F-actin as defined by phalloidin staining was concentrated in expanding pseudopods. Most phalloidin staining was lost as cells rounded up before the onset of flagellum formation. Actin staining with a Naegleria-specific antibody that recognizes both F- and G-actin was confined to the cell cortex of both amebae and flagellates. DNase I demonstrated G-actin throughout all stages. Most of the actin in the cortex was not bound by phalloidin yet was resistant to detergent extraction suggesting that it was polymerized. The microtubule cytoskeleton of flagellates was intimately associated with this actin cortex. Treatment of flagellates with cytochalasin D produced a rapid loss of flagellate shape and the appearance of phalloidin staining while latrunculin A stabilized the flagellate shape. These results suggest that tension produced by an actomyosin network is required to maintain the flagellate shape. The rapid loss of the flagellate shape induced by drugs, which specifically block myosin light chain kinase, supports this hypothesis.     

Genetic investigations on the caffeine and chlorogenic acid relationship in an interspecific cross between Coffea liberica dewevrei and C. pseudozanguebariae

The objective of the paper was to identify the number of major loci explaining caffeine content in coffee seeds. Investigations were based on previously published results: (1) Caffeine binds to chlorogenic acids in a 1:1 molecular ratio; (2) Between species, the caffeine content is correlated to the chlorogenic acid content; (3) Only a part of chlorogenic acids is bound to caffeine. Especially, the content ratio between caffeine and chlorogenic acids varied between species. For identifying the number of major loci, a quantitative trait locus (QTL) approach was carried out using an interspecific cross between two highly differentiated species—Coffea liberica dewevrei and Coffea pseudozanguebariae, the latter being a caffeine-free species. As main finding, two QTLs, i.e., RCQ1 and CQA1, were identified allowing us to explain up to 97 % of the caffeine content variance. RCQ1 explained variation of the caffeine/chlorogenic acid ratio and was genetically independent of the second QTL. The latter explained the part of the caffeine content which was dependent on the chlorogenic acid content. The findings also confirmed that only a part of chlorogenic acids were trapped by caffeine, as in wild species.     

Enzymes of Ornithine-Arginine Metabolism in Trypanosomatids of the Genus Phytomonas1

Trypanosomatids recently isolated from the plants Euphorbia pinea, E. characias, E. hyssopifolia, Manihoi esculenta (cassava) and Lycopersicon sp. (tomato) plus the McGhee-Postell isolate of Phytomonas davidi have been examined for the presence of enzymes of ornithine-arginine metabolism. Arginase (EC 3.5.3.1) was not detected in the flagellates examined whereas arginine deiminase (EC 3.5.3.6) and citrullinehydrolase (EC 3.5.1.20) were present in all organisms. Phytomonas davidi and the isolate from E. hyssopifolia, besides these enzymes, also had ornithine carbamoyltransferase (EC 2.1.3.3). The enzymic constitution of these flagellates is compared from a taxonomic standpoint to that of previously studied trypanosomatids.     

Forest association and phenology of wild coffee in Kibale National Park, Uganda

A study on the forest association and phenology of wild coffee ( Coffea canephora Pierre) was conducted in Kibale forest, Uganda. Nested quadrats were used to enumerate tree species, including coffee and herbaceous plants associated with forest and coffee stands. A total of 150 coffee trees was marked along transects and monthly scans carried out to score for fruits, flowers, leaves and leaf insect damage. Pre- and post-dispersal predation levels and coffee yield estimates were made by examining fruits from trees, forest floor and seasonal fruit falls into demarcated plots. In the forest, wild coffee stands are associated with low-quality forest types in terms of timber species (about 10.5 canopy species/study site) and low stocking densities of trees ≥ 50 cm d.b.h. (average 38 trees ha⁻¹ for each site) and poor forest regeneration. In the forest, wild coffee reproductive phases overlap with ripening, coinciding with flower bud and flower production. The variable peak ripening season falls between November and April. The wild coffee yields are generally low (average of 3.5 intact fruits 16 m⁻² month⁻¹), with low insect fruit/seed damage (4–19%) but high levels of wastage due to monkeys, bats and birds.