Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

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Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

10.21203/rs.3.rs-20034/v2 ◽

2020 ◽

Author(s):

Agata Motyka-Pomagruk ◽

Sabina Zoledowska ◽

Agnieszka Emilia Misztak ◽

Wojciech Sledz ◽

Alessio Mengoni ◽

...

Keyword(s):

Comparative Genomics ◽

Large Scale ◽

De Novo ◽

Genetic Material ◽

Soft Rot ◽

Potato Production ◽

Core Gene ◽

Ecological Niches ◽

Dickeya Solani ◽

High Level

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Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

10.21203/rs.3.rs-20034/v1 ◽

2020 ◽

Author(s):

Agata Motyka-Pomagruk ◽

Sabina Zoledowska ◽

Agnieszka Emilia Misztak ◽

Wojciech Sledz ◽

Alessio Mengoni ◽

...

Keyword(s):

Large Scale ◽

De Novo ◽

Genetic Material ◽

Soft Rot ◽

Potato Production ◽

Core Gene ◽

Ecological Niches ◽

Dickeya Solani ◽

Scientific Attention ◽

High Level

Abstract Background: Dickeya solani was pointed as a significant trait to potato production in Europe and drew much of scientific attention due to remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In a view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a nearly conclusive pangenome analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes sequences and the sequences of 14 additional strains revealed exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories revealed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic for taxa, whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal spread and population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny was found, which might reflect the specificity of the international seed potato market.

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Unlocking the Potential of 46 New Bacteriophages for Biocontrol of Dickeya Solani

Viruses ◽

10.3390/v10110621 ◽

2018 ◽

Vol 10 (11) ◽

pp. 621 ◽

Cited By ~ 16

Author(s):

Alexander Carstens ◽

Amaru Djurhuus ◽

Witold Kot ◽

Deborah Jacobs-Sera ◽

Graham Hatfull ◽

...

Keyword(s):

Soft Rot ◽

Potato Production ◽

Storage Conditions ◽

Bacterial Diseases ◽

Modern Agriculture ◽

Production Pipeline ◽

Global Demand ◽

Phage Cocktail ◽

Dickeya Solani ◽

Sustainability Standards

Modern agriculture is expected to face an increasing global demand for food while also needing to comply with higher sustainability standards. Therefore, control of crop pathogens requires new, green alternatives to current methods. Potatoes are susceptible to several bacterial diseases, with infections by soft rot Enterobacteriaceae (SRE) being a significant contributor to the major annual losses. As there are currently no efficient ways of combating SRE, we sought to develop an approach that could easily be incorporated into the potato production pipeline. To this end, 46 phages infecting the emerging potato pathogen Dickeya solani were isolated and thoroughly characterized. The 46 isolated phages were grouped into three different groups based on DNA similarity, representing two distinct clusters and a singleton. One cluster showed similarity to phages previously used to successfully treat soft rot in potatoes, whereas the remaining phages were novel and showed only very limited similarity to previously isolated phages. We selected six diverse phages in order to create the hereto most complex phage cocktail against SRE. The cocktail was applied in a proof-of-principle experiment to treat soft rot in potatoes under simulated storage conditions. We show that the phage cocktail was able to significantly reduce the incidence of soft rot as well as disease severity after 5 days of storage post-infection with Dickeya solani. This confirms results from previous studies that phages represent promising biocontrol agents against SRE infection in potato.

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First Report of Dickeya solani Causing Soft Rot in Imported Bulbs of Hyacinthus orientalis in China

Plant Disease ◽

10.1094/pdis-09-14-0916-pdn ◽

2015 ◽

Vol 99 (1) ◽

pp. 155-155 ◽

Cited By ~ 4

Author(s):

X. F. Chen ◽

H. L. Zhang ◽

J. Chen

Keyword(s):

16S Rrna ◽

The Netherlands ◽

Bacterial Pathogen ◽

Soft Rot ◽

Potato Production ◽

Sterile Water ◽

First Report ◽

Hyacinthus Orientalis ◽

Dickeya Solani ◽

Negative Controls

A bacterial pathogen, Dickeya solani, emerged as a major threat to potato (Solanum tuberosum) production in Europe in 2004 and has spread to many potato-growing regions via international trade. In December 2013, soft rot symptoms were observed in hyacinth (Hyacinthus orientalis) bulbs imported from the Netherlands into China at Ningbo Port. Diseased bulbs gave off an offensive odor. The base and internal parts of diseased bulbs rotted, and the margins of diseased tissues showed brown discoloration. Isolation on nutrient agar glucose (NAG) medium resulted in dominating colonies of characteristic “fried egg” morphology (1). One colony was chosen for further investigation and tentatively named “isolate 6165-3.” Under microscopic visualization after gram stain, the cells of isolate 6165-3 were gram-negative, motile, and rod shaped. The isolate was then identified as a member of genus Dickeya using the Biolog GN microplate. The 16S rRNA, recA, and dnaX sequences of isolate 6165-3 were subsequently determined and deposited in GenBank with accession numbers KM405240, KM405241, and KM405242, sharing 99% (16S rRNA), 100% (recA), and 100% (dnaX) nucleotide identity with those of known D. solani isolates, respectively. By this means, the isolate 6165-3 was identified as D. solani (1,2). To confirm the pathogenicity of the isolate, four plants each of 30-day-old hyacinth, 14-day-old potato, and 60-day-old moth orchid (Phalaenopsis amabilis) were inoculated with suspensions of the isolate with a concentration of 108 CFU/ml in sterile water by stabbing. Plants were incubated in a climate chamber at 28°C during the day and 24°C during the night with a relative humidity of 93% and a photoperiod of 12/12 h. Plants inoculated with sterile water were included as negative controls. After 2 or 3 days, typical symptoms such as water-soaked lesions and soft rot developed around the inoculation point, while the negative controls remained symptomless. Koch's postulates were fulfilled by re-isolating bacteria from lesions, which had identical sequence and morphology characters with the inoculated isolate. This is the first report of intercepted D. solani on hyacinth bulbs imported from the Netherlands into China, indicating that D. solani can spread via hyacinth. Further spread of the pathogen into potato production might lead to immeasurable economic consequences for China. References: (1) P. F. Sarris et al. New Dis. Rep. 24:21, 2011. (2) J. M. van der Wolf et al. Int. J. Syst. Evol. Microbiol. 64:768, 2014.

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Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia

PLoS ONE ◽

10.1371/journal.pone.0243853 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243853

Author(s):

Berline Fopa Fomeju ◽

Dominique Brunel ◽

Aurélie Bérard ◽

Jean-Baptiste Rivoal ◽

Philippe Gallois ◽

...

Keyword(s):

Large Scale ◽

De Novo ◽

Rapid Development ◽

Genetic Distances ◽

Lavandula Angustifolia ◽

Distance Analysis ◽

Alternative Medicines ◽

Dna And Rna ◽

Snp Development ◽

High Level

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone “Maillette” was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

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The occurrence of bacteria from different species of Pectobacteriaceae on seed potato plantations in Poland

European Journal of Plant Pathology ◽

10.1007/s10658-020-02163-x ◽

2020 ◽

Author(s):

Agata Motyka-Pomagruk ◽

Sabina Zoledowska ◽

Wojciech Sledz ◽

Ewa Lojkowska

Keyword(s):

Seed Potato ◽

Soft Rot ◽

Potato Production ◽

Potato Cultivars ◽

Economic Losses ◽

Growing Seasons ◽

Causative Agents ◽

Dickeya Solani ◽

Reported Data ◽

June July

AbstractBacteria from the genera Dickeya and Pectobacterium, the causative agents of soft rot and blackleg, trigger significant economic losses in potato production worldwide. Efficient struggle with these phytopathogens is highly challenging taking into consideration the lack of available control procedures. As only preventive measures are accessible, we decided to provide insight into the soft rot Pectobacteriaceae (SRP) present in Poland. During the growing seasons of 2013 and 2014, altogether 531 potato plants were collected from 138 seed potato fields and 23 storage facilities. Plant origin of the isolated bacteria, frequencies of coinfections with different species, the affected potato cultivars in addition to seasonal variation in the occurrence of SRP were studied. It was shown that bacteria from the Pectobacterium genus were abundant and outnumbered the ones classified to Dickeya spp. The vast majority of strains was isolated from the plant samples collected in July 2013 or in June–July 2014. The presence of all taxa of interest: Pectobacterium atrosepticum, Pectobacterium carotovorum, Pectobacterium parmentieri, Dickeya dianthicola and Dickeya solani were confirmed in July each year. We were able to isolate bacteria from the genus Dickeya and Pectobacterium from 35 out of 58 potato cultivars tested. The majority of SRP was isolated from potato stems, not from potato tubers. In four cases, coinfections of potato samples with even three diverse species of SRP, i.e. P. atrosepticum, P. carotovorum and P. parmentieri, were noted. It seems that since the first documented appearance of Dickeya solani in Poland in 2005, this pathogen has not played a dominating role in our country. The reported data describing the appearance and distribution of SRP in Poland might allow for prediction of the risks associated with infections initiated by these bacteria.

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Novel generation of human satellite DNA-based artificial chromosomes in mammalian cells

Journal of Cell Science ◽

10.1242/jcs.113.18.3207 ◽

2000 ◽

Vol 113 (18) ◽

pp. 3207-3216 ◽

Cited By ~ 1

Author(s):

E. Csonka ◽

I. Cserpan ◽

K. Fodor ◽

G. Hollo ◽

R. Katona ◽

...

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Mammalian Cells ◽

Large Scale ◽

De Novo ◽

Mammalian Species ◽

Genetic Material ◽

Exogenous Dna ◽

Artificial Chromosomes ◽

Acrocentric Chromosomes

An in vivo approach has been developed for generation of artificial chromosomes, based on the induction of intrinsic, large-scale amplification mechanisms of mammalian cells. Here, we describe the successful generation of prototype human satellite DNA-based artificial chromosomes via amplification-dependent de novo chromosome formations induced by integration of exogenous DNA sequences into the centromeric/rDNA regions of human acrocentric chromosomes. Subclones with mitotically stable de novo chromosomes were established, which allowed the initial characterization and purification of these artificial chromosomes. Because of the low complexity of their DNA content, they may serve as a useful tool to study the structure and function of higher eukaryotic chromosomes. Human satellite DNA-based artificial chromosomes containing amplified satellite DNA, rDNA, and exogenous DNA sequences were heterochromatic, however, they provided a suitable chromosomal environment for the expression of the integrated exogenous genetic material. We demonstrate that induced de novo chromosome formation is a reproducible and effective methodology in generating artificial chromosomes from predictable sequences of different mammalian species. Satellite DNA-based artificial chromosomes formed by induced large-scale amplifications on the short arm of human acrocentric chromosomes may become safe or low risk vectors in gene therapy.

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The phytopathogenic nature ofDickeya aquatica174/2 and the dynamic early evolution ofDickeyapathogenicity

10.1101/568105 ◽

2019 ◽

Author(s):

Alexandre Duprey ◽

Najwa Taib ◽

Simon Leonard ◽

Tiffany Garin ◽

Jean-Pierre Flandrois ◽

...

Keyword(s):

Complete Genome ◽

Type Strain ◽

Large Scale ◽

Plant Cell Wall ◽

Soft Rot ◽

Phylogenetic Position ◽

Ecological Niches ◽

Phylogenomic Analysis ◽

Cell Wall Degrading Enzymes ◽

Patterns And Processes

AbstractOriginality-Significance statementAlthough the reach of large-scale comparative studies has spread exponentially over the years, the phytopathogenicDickeyagroup remains overlooked. In this work, we sequence the complete genome ofDickeya aquaticatype strain, a species isolated from water that was first assumed to be non-phytopathogenic. We show that the proteome ofD. aquaticacontains a wide number of proteins involved inDickeyavirulence, including plant cell wall degrading enzymes, suggesting that this species could be in fact pathogenic. Using experimental approaches, we confirm this prediction and uncover the particular affinity ofD. aquaticafor acidic fruits. In-depth phylogenomic analyses reveal thatDickeyaspecies display a great degree of genetic plasticity in the pathogenicity determinants, explaining how this bacterial group was able to colonize a wide variety of plants growing in different climates. These observations greatly advance our understanding of how bacteria adapt to new ecological niches.SummaryDickeyais a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus,Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, whileD. aquaticawas proposed to represent a deep-branching species amongDickeyagenus, its precise phylogenetic position remained elusive.Here, we report the complete genome sequence of theD. aquaticatype strain 174/2. We demonstrate the affinity ofD. aquaticaTfor acidic fruits such as tomato and cucumber, and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all availableDickeyaproteomes pinpointsD. aquaticaas the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.):Dickeyags. poaceaephila (Dickeyasp NCPPB 569) andDickeyags. undicola (Dickeyasp 2B12), together with a new putative genus, tentatively namedProdigiosinella. Finally, from comparative analyses ofDickeyaproteomes we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes ofDickeyato different environmental niches and hosts. In particular, we hypothetize that the lack of xylanases and xylose degradation pathways inD. aquaticacould reflects adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

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Combining natural language processing and metabarcoding to reveal pathogen-environment associations

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0008755 ◽

2021 ◽

Vol 15 (4) ◽

pp. e0008755

Author(s):

David C. Molik ◽

DeAndre Tomlinson ◽

Shane Davitt ◽

Eric L. Morgan ◽

Matthew Sisk ◽

...

Keyword(s):

Natural Language Processing ◽

Natural Language ◽

Language Processing ◽

Large Scale ◽

Topic Model ◽

De Novo ◽

Sub Saharan Africa ◽

Ecological Niches ◽

Allocation Model ◽

Model Sets

Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year—with 180,000 resulting deaths—mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C. neoformans in nature. To expand our understanding of the distribution and ecological associations of this pathogen we implement a Natural Language Processing approach to better describe the niche of C. neoformans. We use a Latent Dirichlet Allocation model to de novo topic model sets of metagenetic research articles written about varied subjects which either explicitly mention, inadvertently find, or fail to find C. neoformans. These articles are all linked to NCBI Sequence Read Archive datasets of 18S ribosomal RNA and/or Internal Transcribed Spacer gene-regions. The number of topics was determined based on the model coherence score, and articles were assigned to the created topics via a Machine Learning approach with a Random Forest algorithm. Our analysis provides support for a previously suggested linkage between C. neoformans and soils associated with decomposing wood. Our approach, using a search of single-locus metagenetic data, gathering papers connected to the datasets, de novo determination of topics, the number of topics, and assignment of articles to the topics, illustrates how such an analysis pipeline can harness large-scale datasets that are published/available but not necessarily fully analyzed, or whose metadata is not harmonized with other studies. Our approach can be applied to a variety of systems to assert potential evidence of environmental associations.

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Quick and efficient approach to develop genomic resources in orphan species: application in Lavandula angustifolia

10.1101/381400 ◽

2018 ◽

Author(s):

Berline Fopa Fomeju ◽

Dominique Brunel ◽

Aurélie Bérard ◽

Jean-Baptiste Rivoal ◽

Philippe Gallois ◽

...

Keyword(s):

Large Scale ◽

De Novo ◽

Rapid Development ◽

Genetic Distances ◽

Lavandula Angustifolia ◽

Alternative Medicines ◽

Snp Development ◽

High Level ◽

The Cost ◽

Next Generation Sequencing Ngs

AbstractNext-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors of research efforts to generate genomic data to a range of previously poorly studied species. In this study, we proposed a method for the rapid development of a large scale molecular resources for orphan species. We studied as an example Lavandula angustifolia, a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines.We first built a ‘Maillette’ reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with exons and introns) using a transcriptome-guided DNA-seq assembly approach in order to maximize the possibilities of finding polymorphism between genetically close individuals. Finally, we used these resources for SNP mining within a collection of 16 lavender clones and tested the SNP within the scope of a phylogeny analysis. We obtained a cleaned reference of 8, 030 functionally annotated ‘genes’ (in silico annotation). We found up to 400K polymorphic sites, depending on the genotype analyzed, and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). We found similar genetic distances between pairs of clones, related to the out-crossing nature of the species, the restricted area of cultivation and the clonal propagation of the varieties.The method propose is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is the first reported large-scale SNP development on Lavandula angustifolia. All this data provides a rich pool of molecular resource to explore and exploit biodiversity in breeding programs.

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