Complete Genome Sequence of the plant pathogenic fungus Colletotrichum lupini.

Colletotrichum is a fungal genus (Ascomycota, Sordariomycetes, Glomerellaceae) that includes many economically important plant pathogens that cause devastating diseases of a wide range of plants. In this work, using a combination of long and short-read sequencing technologies, we sequenced the genome of Colletotrichum lupini RB221, isolated from white lupin (Lupinus albus) in France during a survey in 2014. The genome was assembled into eleven nuclear chromosomes and a mitochondrial genome with a total assembly size of 63.41Mb and 36.55 Kb, respectively. A total of 18324 protein encoding genes have been predicted, of which only 39 are specific to C. lupini. To the best of our knowledge this is the first genome of this species to be fully sequenced and to get publicly released. This resource will provide insight into pathogenicity factors and will help to get a better understanding of the evolution and genome structure of this important plant pathogen.

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Dwarfism does not modify mean area per leaf and light interception in indeterminate autumn-sown white lupin

The Journal of Agricultural Science ◽

10.1017/s0021859600078515 ◽

1996 ◽

Vol 127 (3) ◽

pp. 337-345 ◽

Cited By ~ 3

Author(s):

N. Harzic ◽

C. Huyghe

Keyword(s):

Lupinus Albus ◽

Leaf Size ◽

Branch Length ◽

Light Interception ◽

White Lupin ◽

Low Light ◽

First Order ◽

Logistic Equations ◽

Wide Range ◽

Number Of Leaves

SUMMARYThe effect of dwarfism on leaf number and size was investigated on six pairs of tall and dwarf nearisogenic lines of indeterminate autumn-sown white lupins (Lupinus albus L.). Dwarfism reduced mainstem height by 41% and first-order branch length by 22%. It also slightly decreased the number of leaves on the mainstem and first-order branches without affecting the time of flowering. Leaf size was not reduced. Logistic equations were used to analyse differences in the patterns of light interception by leaf canopies relative to thermal time from sowing during the growth of seven dwarf lines and three tall cultivars sown on different dates. The genotypes studied had long periods of low light interception during their early growth. No differences were found between most of the equation parameters for dwarf and tall genotypes. Only the proportion of light intercepted at flowering differed and this was explained by differences in flowering time. The dwarf character did not limit the ability of the crop canopies to intercept light. It is concluded that the character can be introduced into a wide range of genetic backgrounds without deleterious effects.

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White Lupin (Lupinus albus L. cv. Amiga) Increases Solubility of Minjingu Phosphate Rock, Phosphorus Balances and Maize Yields in Njoro Kenya

Sustainable Agriculture Research ◽

10.5539/sar.v3n3p37 ◽

2014 ◽

Vol 3 (3) ◽

pp. 37 ◽

Cited By ~ 3

Author(s):

Joyce J. Lelei ◽

Richard N. Onwonga

Keyword(s):

Grain Yield ◽

Phosphate Rock ◽

Block Design ◽

Lupinus Albus ◽

Farming Systems ◽

White Lupin ◽

Wide Range ◽

Maize Yields ◽

Lupinus Albus L ◽

Minjingu Phosphate Rock

Exudation of high amounts of citrate in white lupin (Lupinus albus L. cv. Amiga) has the advantage of being effective in mobilization of a wide range of sparingly soluble P sources. To improve cultivation system of maize, a field experiment was conducted to assess effectiveness of white lupin (Lupinus albus L. cv. Amiga) in increasing solubility of minjingu phosphate rock (MPR), phosphorus balances and maize yields in Njoro sub-County, Kenya. The randomized complete block design experiment was conducted for four seasons; short (October – February) and long rain seasons (March-September) of 2010 and 2011. The treatments were; (i) fallow (F) – maize (M) rotation with triple superphosphate (TSP) applied (MTSP- F), (ii) fallow - maize rotation with MPR applied (MMPR –F), (iii) lupin (L) – maize rotation with MPR applied (MMPR- L) and (iv) maize/lupin intercrop with MPR applied (M/LMPR – F). Soil and plant P and maize grain yield were higher in M/LMPR – F (with additional lupin grain yield) and MTSP– F treatments. All treatments resulted in positive P balances at the end of two years with highest values in MTSP– F treatment and lowest in M/LMPR – F. Intercropping lupin with maize amid application of MPR is recommended for enhanced maize performance in the farming systems of resource poor farmers. Measurement of available soil nitrogen and comparison of lupin with other legumes in solubilizing MPR is recommended.

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Complete Genome Sequence of the Biocontrol Agent YeastRhodotorula kratochvilovaeStrain LS11

Genome Announcements ◽

10.1128/genomea.00120-18 ◽

2018 ◽

Vol 6 (10) ◽

Cited By ~ 2

Author(s):

Cecilia Miccoli ◽

Davide Palmieri ◽

Filippo De Curtis ◽

Giuseppe Lima ◽

Giuseppe Ianiri ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Complete Genome Sequence ◽

Genome Annotation ◽

Complete Genome ◽

Plant Pathogens ◽

Biocontrol Agent ◽

Antagonistic Activity ◽

Protein Encoding ◽

Encoding Genes

ABSTRACTRhodotorula kratochvilovaestrain LS11 is a biocontrol agent (BCA) selected for its antagonistic activity against several plant pathogens both in the field and postharvest. Genome assembly includes 62 contigs for a total of 22.56 Mbp and a G+C content of 66.6%. Genome annotation predicts 7,642 protein-encoding genes.

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Meta-Omics Tools in the World of Insect-Microorganism Interactions

Biology ◽

10.3390/biology7040050 ◽

2018 ◽

Vol 7 (4) ◽

pp. 50 ◽

Cited By ~ 5

Author(s):

Antonino Malacrinò

Keyword(s):

Safety Assessment ◽

Plant Pathogens ◽

Lower Cost ◽

Insect Pests ◽

Fungal Communities ◽

Microbial World ◽

Sequencing Technologies ◽

Wide Range ◽

The World ◽

User Friendly

Microorganisms are able to influence several aspects of insects’ life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies are now available at a lower cost per base, and bioinformatic procedures are becoming more user-friendly. This is triggering a huge effort in studying the microbial diversity associated to insects, and especially to economically important insect pests. The importance of the microbiome has been widely acknowledged for a wide range of animals, and also for insects this topic is gaining considerable importance. In addition to bacterial-associates, the insect-associated fungal communities are also gaining attention, especially those including plant pathogens. The use of meta-omics tools is not restricted to the description of the microbial world, but it can be also used in bio-surveillance, food safety assessment, or even to bring novelties to the industry. This mini-review aims to give a wide overview of how meta-omics tools are fostering advances in research on insect-microorganism interactions.

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Mixed-Species Genomic Microarray Analysis of Fecal Samples Reveals Differential Transcriptional Responses of Bifidobacteria in Breast- and Formula-Fed Infants

Applied and Environmental Microbiology ◽

10.1128/aem.02492-08 ◽

2009 ◽

Vol 75 (9) ◽

pp. 2668-2676 ◽

Cited By ~ 78

Author(s):

Eline S. Klaassens ◽

Rolf J. Boesten ◽

Monique Haarman ◽

Jan Knol ◽

Frank H. Schuren ◽

...

Keyword(s):

Denaturing Gradient Gel Electrophoresis ◽

Rrna Genes ◽

Transcriptional Responses ◽

Fecal Samples ◽

Young Infants ◽

Exact Function ◽

Wide Range ◽

Protein Encoding ◽

Encoding Genes

ABSTRACT Although their exact function remains enigmatic, bifidobacteria are among the first colonizers of the newborn infant gut and further develop into abundant communities, notably in response to diet. Therefore, the transcriptional responses of bifidobacteria in rapidly processed fecal samples from young infants that were fed either breast milk or a formula containing a mixture of galacto- and fructo-oligosaccharides were studied. The presence and diversity of the bifidobacterial fecal communities were determined using PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR for specific species. Changes in the total number of bifidobacteria as well as in species diversity were observed, indicating the metabolic activities of the bifidobacteria within the infant gut. In addition, total RNAs isolated from infant feces were labeled and hybridized to a bifidobacterium-specific microarray comprising approximately 6,000 clones of the major bifidobacterial species of the human gut. Approximately 270 clones that showed the most prominent hybridization with the samples were sequenced. Fewer than 10% of the hybridizing clones contained rRNA genes, whereas the vast majority of the inserts showed matches with protein-encoding genes predicted to originate from bifidobacteria. Although a wide range of functional groups was covered by the obtained sequences, the largest fraction (14%) of the transcribed genes assigned to a functional category were predicted to be involved in carbohydrate metabolism, while some were also implicated in exopolysaccharide production or folate production. A total of three of the above-described protein-encoding genes were selected for quantitative PCR and sequence analyses, which confirmed the expression of the corresponding genes and the expected nucleotide sequences. In conclusion, the results of this study show the feasibility of obtaining insight into the transcriptional responses of intestinal bifidobacteria by analyzing fecal RNA and highlight the in vivo expression of bifidobacterial genes implicated in host-related functions.

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A qPCR Assay for the Fast Detection and Quantification of Colletotrichum lupini

Plants ◽

10.3390/plants10081548 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1548

Author(s):

Tim Kamber ◽

Nachelli Malpica-López ◽

Monika M. Messmer ◽

Thomas Oberhänsli ◽

Christine Arncken ◽

...

Keyword(s):

Lupinus Albus ◽

Qpcr Assay ◽

White Lupin ◽

Infected Seed ◽

Legume Crop ◽

Mother Plants ◽

Lupin Seeds ◽

Infection Source ◽

Colletotrichum Lupini ◽

Detection And Quantification

White lupin (Lupinus albus) represents an important legume crop in Europe and other parts of the world due to its high protein content and potential for low-input agriculture. However, most cultivars are susceptible to anthracnose caused by Colletotrichum lupini, a seed- and air-borne fungal pathogen that causes severe yield losses. The aim of this work was to develop a C. lupini-specific quantitative real-time TaqMan PCR assay that allows for quick and reliable detection and quantification of the pathogen in infected seed and plant material. Quantification of C. lupini DNA in dry seeds allowed us to distinguish infected and certified (non-infected) seed batches with DNA loads corresponding to the disease score index and yield of the mother plants. Additionally, C. lupini DNA could be detected in infected lupin shoots and close to the infection site, thereby allowing us to study the disease cycle of this hemibiotrophic pathogen. This qPCR assay provides a useful diagnostic tool to determine anthracnose infection levels of white lupin seeds and will facilitate the use of seed health assessments as a strategy to reduce the primary infection source and spread of this disease.

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Complete Genome Sequence of the Biocontrol Yeast Papiliotrema terrestris Strain LS28

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab332 ◽

2021 ◽

Author(s):

Davide Palmieri ◽

Giuseppe Barone ◽

Riccardo Aiese Cigliano ◽

Filippo De Curtis ◽

Giuseppe Lima ◽

...

Keyword(s):

Genome Annotation ◽

Plant Pathogens ◽

Biocontrol Agent ◽

Antagonistic Activity ◽

Whole Genome ◽

Genome Data ◽

A Genome ◽

Protein Encoding ◽

Genetic Mechanisms ◽

Encoding Genes

Abstract Papiliotrema terrestris strain LS28 is a biocontrol agent (BCA) selected for its antagonistic activity against several plant pathogens both in the field and postharvest. The availability of a genome sequencing sets the foundation for the identification of the genetic mechanisms of its antagonistic activity. The genome size is 21.29 Mbp with a G + C content of 58.65%, and genome annotation predicts 8,626 protein-encoding genes. Phylogenetic analysis based on whole genome data confirms that P. terrestris is a Tremellomycetes more closely related to P. flavescens than P. laurentii.

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Studies on the EC50 of Natural Monoterpenes as Fungal Inhibitors with Quantitative Structure-Activity Relationships (QSARs)

The Natural Products Journal ◽

10.2174/2210315509666190117150153 ◽

2020 ◽

Vol 10 (1) ◽

pp. 44-60

Author(s):

Mohamed E.I. Badawy ◽

Entsar I. Rabea ◽

Samir A.M. Abdelgaleil

Keyword(s):

Biological Activity ◽

Plant Pathogens ◽

Molecular Descriptors ◽

Microbial Pathogens ◽

Quantitative Structure ◽

Qsar Study ◽

Qsar Analysis ◽

Pharmacophore Modelling ◽

Structure Activity ◽

Wide Range

Background:Monoterpenes are the main constituents of the essential oils obtained from plants. These natural products offered wide spectra of biological activity and extensively tested against microbial pathogens and other agricultural pests.Methods:Antifungal activity of 10 monoterpenes, including two hydrocarbons (camphene and (S)- limonene) and eight oxygenated hydrocarbons ((R)-camphor, (R)-carvone, (S)-fenchone, geraniol, (R)-linalool, (+)-menthol, menthone, and thymol), was determined against fungi of Alternaria alternata, Botrytis cinerea, Botryodiplodia theobromae, Fusarium graminearum, Phoma exigua, Phytophthora infestans, and Sclerotinia sclerotiorum by the mycelia radial growth technique. Subsequently, Quantitative Structure-Activity Relationship (QSAR) analysis using different molecular descriptors with multiple regression analysis based on systematic search and LOOCV technique was performed. Moreover, pharmacophore modelling was carried out using LigandScout software to evaluate the common features essential for the activity and the hypothetical geometries adopted by these ligands in their most active forms.Results:The results showed that the antifungal activities were high, but depended on the chemical structure and the type of microorganism. Thymol showed the highest effect against all fungi tested with respective EC50 in the range of 10-86 mg/L. The QSAR study proved that the molecular descriptors HBA, MR, Pz, tPSA, and Vp were correlated positively with the biological activity in all of the best models with a correlation coefficient (r) ≥ 0.98 and cross-validated values (Q2) ≥ 0.77.Conclusion:The results of this work offer the opportunity to choose monoterpenes with preferential antimicrobial activity against a wide range of plant pathogens.

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Control of Winged Waterprimrose (Jussiaea decurrens) and Northern Jointvetch (Aeschynomene virginica) with Fungal Pathogens

Weed Science ◽

10.1017/s0043174500044477 ◽

1979 ◽

Vol 27 (5) ◽

pp. 497-501 ◽

Cited By ~ 46

Author(s):

C. D. Boyette ◽

G. E. Templeton ◽

R. J. Smith

Keyword(s):

Oryza Sativa ◽

Glycine Max ◽

Fungal Pathogens ◽

Liquid Culture ◽

Field Experiments ◽

Colletotrichum Gloeosporioides ◽

Pathogenic Fungus ◽

Field Tests ◽

Wide Range ◽

Growing Region

An indigenous, host-specific, pathogenic fungus that parasitizes winged waterprimrose [Jussiaea decurrens(Walt.) DC.] is endemic in the rice growing region of Arkansas. The fungus was isolated and identified asColletotrichum gloeosporioides(Penz.) Sacc. f.sp. jussiaeae(CGJ). It is highly specific for parasitism of winged waterprimrose and not parasitic on creeping waterprimrose (J. repensL. var.glabrescensKtze.), rice (Oryza sativaL.), soybeans [Glycine max(L.) Merr.], cotton (Gossypium hirsutumL.), or 4 other crops and 13 other weeds. The fungus was physiologically distinct from C.gloeosporioides(Penz.) Sacc. f. sp.aeschynomene(CGA), an endemic anthracnose pathogen of northern jointvetch[Aeschynomene virginica(L.) B.S.P.], as indicated by cross inoculations of both weeds. Culture in the laboratory and inoculation of winged waterprimrose in greenhouse, growth chamber and field experiments indicated that the pathogen was stable, specific, and virulent in a wide range of environments. The pathogen yielded large quantities of spores in liquid culture. It is suitable for control of winged waterprimrose. Winged waterprimrose and northern jointvetch were controlled in greenhouse and field tests by application of spore mixtures of CGJ and CGA at concentrations of 1 to 2 million spores/ml of each fungus in 94 L/ha of water; the fungi did not damage rice or nontarget crops.

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Quantitative Control of Early Flowering in White Lupin (Lupinus albus L.)

International Journal of Molecular Sciences ◽

10.3390/ijms22083856 ◽

2021 ◽

Vol 22 (8) ◽

pp. 3856

Author(s):

Sandra Rychel-Bielska ◽

Anna Surma ◽

Wojciech Bielski ◽

Bartosz Kozak ◽

Renata Galek ◽

...

Keyword(s):

Flowering Time ◽

Association Studies ◽

Lupinus Albus ◽

Genotypic Diversity ◽

Early Flowering ◽

White Lupin ◽

Genome Wide Association Studies ◽

Interacting Protein ◽

Major Qtls ◽

Lupinus Albus L

White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection.

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