Browsing by Subject "Phylogeny"

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Diagnostics and genome analysis of phloem-limited phytopathogenic bacteria
(2022) Zübert, Christina; Hölzle, Ludwig
This thesis contributes to improving the epidemiological understanding of ‘Candidatus Arsenophonus phytopathogenicus’ and bacteria of the provisional taxon ‘Candidatus Phytoplasma’ by applying genetic markers for identification, differentiation, and phylogenetic reconstruction of this economically relevant plant pathogens.
Divergence within the taxon ‘Candidatus Phytoplasma asteris’ confirmed by comparative genome analysis of carrot strains
(2024) Toth, Rafael; Ilic, Anna-Marie; Huettel, Bruno; Duduk, Bojan; Kube, Michael
Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon ‘Candidatus Phytoplasma asteris’ were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of ‘Ca. P. asteris’ and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.
The functional diversity of the high-affinity nitrate transporter gene family in hexaploid wheat: Insights from distinct expression profiles
(2023) Sigalas, Petros P.; Buchner, Peter; Kröper, Alex; Hawkesford, Malcolm J.
High-affinity nitrate transporters (NRT) are key components for nitrogen (N) acquisition and distribution within plants. However, insights on these transporters in wheat are scarce. This study presents a comprehensive analysis of the NRT2 and NRT3 gene families, where the aim is to shed light on their functionality and to evaluate their responses to N availability. A total of 53 NRT2s and 11 NRT3s were identified in the bread wheat genome, and these were grouped into different clades and homoeologous subgroups. The transcriptional dynamics of the identified NRT2 and NRT3 genes, in response to N starvation and nitrate resupply, were examined by RT-qPCR in the roots and shoots of hydroponically grown wheat plants through a time course experiment. Additionally, the spatial expression patterns of these genes were explored within the plant. The NRT2s of clade 1, TaNRT2.1-2.6, showed a root-specific expression and significant upregulation in response to N starvation, thus emphasizing a role in N acquisition. However, most of the clade 2 NRT2s displayed reduced expression under N-starved conditions. Nitrate resupply after N starvation revealed rapid responsiveness in TaNRT2.1-2.6, while clade 2 genes exhibited gradual induction, primarily in the roots. TaNRT2.18 was highly expressed in above-ground tissues and exhibited distinct nitrate-related response patterns for roots and shoots. The TaNRT3 gene expression closely paralleled the profiles of TaNRT2.1-2.6 in response to nitrate induction. These findings enhance the understanding of NRT2 and NRT3 involvement in nitrogen uptake and utilization, and they could have practical implications for improving nitrogen use efficiency. The study also recommends a standardized nomenclature for wheat NRT2 genes, thereby addressing prior naming inconsistencies.
Mating-type analysis in Diaporthe isolates from soybean in central Europe
(2025) Hosseini, Behnoush; Käfer, Lena Sophia; Link, Tobias Immanuel; Cai, Lei
Species of the genus Diaporthe have a mating-type system with the two mating types MAT1-1 and MAT1-2, like other ascomycetes. They can either be heterothallic, which means that any isolate only possesses one of the two mating types and needs a mating partner for sexual reproduction, or homothallic, which means that they possess both mating types and are self-fertile. For several Diaporthe species, no sexual reproduction has been observed so far. Using PCR with primers specific to the defining genes MAT1-1-1 and MAT1-2-1 , we determined the mating types of 33 isolates of Diaporthe caulivora , D. eres , D. longicolla , and D. novem from central Europe. In addition, we partially sequenced the mating-type genes of 25 isolates. We found that different D. longicolla isolates either possess MAT1-1-1 or MAT1-2-1, making the species heterothallic, which is in contrast to previous studies and the general assumption that D. longicolla only reproduces asexually. D. eres and D. novem were also found to be heterothallic. Using genomic sequence information and re-sequencing of DNA and RNA, we identified the MAT1-1-1 gene in D. caulivora and present here the full sequence of the mating-type locus of this homothallic species. Finally, we used sequence information from MAT1-1-1 and MAT1-2-1 , respectively, for improved phylogenetic resolution of our isolates.
Peronospora aquilegiicola made its way to Germany: The start of a new pandemic?
(2020) Thines, Marco; Buaya, Anthony; Ali, Tahir; Brand, Thomas
Peronospora aquilegiicola is a destructive pathogen of columbines and has wiped out most Aquilegia cultivars in several private and public gardens throughout Britain. The pathogen, which is native to East Asia was noticed in England and Wales in 2013 and quickly spread through the country, probably by infested plants or seeds. To our knowledge, the pathogen has so far not been reported from other parts of Europe. Here, we report the emergence of the pathogen in the northwest of Germany, based on morphological and phylogenetic evidence. As the pathogen was found in a garden in which no new columbines had been planted recently, we assume that the pathogen has already spread from its original point of introduction in Germany. This calls for an increased attention to the further spread of the pathogen and the eradication of infection spots to avoid the spread to naturally occurring columbines in Germany and to prevent another downy mildew from becoming a global threat, like Peronospora belbahrii and Plasmopara destructor, the downy mildews of basil and balsamines, respectively.
The 16SrXII-P phytoplasma GOE is separated from other stolbur phytoplasmas by key genomic features
(2025) Toth, Rafael; Huettel, Bruno; Varrelmann, Mark; Kube, Michael; Toth, Rafael; Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany;; Huettel, Bruno; Max Planck-Genome-Center Cologne, 50829 Cologne, Germany;; Varrelmann, Mark; Institute of Sugar Beet Research (IfZ), 37079 Göttingen, Germany;; Kube, Michael; Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany;; Kizheva, Yoana; Hristova, Petya
The syndrome “bassess richesses” is a vector-borne disease of sugar beet in Germany. The gammaproteobacterium ‘ Candidatus Arsenophonus phytopathogenicus’ causes reduced sugar content and biomass, growth abnormalities, and yellowing. Co-infection with the 16SrXII-P stolbur phytoplasmas often leads to more severe symptoms and a risk of complete economic loss. This yellowing agent of the Mollicutes class had not been described before, so its differences from other stolbur phytoplasmas remained unanswered. The genome of strain GOE was sequenced, providing a resource to analyze its characteristics. Phylogenetic position was revised, genome organization was compared, and functional reconstructions of metabolic and virulence factors were performed. Average nucleotide identity analysis indicates that GOE represents a new ‘ Ca. Phytoplasma’ species. Our results show that GOE is also distinct from other stolbur phytoplasmas in terms of smaller genome size and G+C content. Its reductive evolution is reflected in conserved membrane protein repertoire and minimal metabolism. The encoding of a riboflavin kinase indicates a lost pathway of phytoplasmas outside the groups 16SrXII and 16SrXIII. GOE shows a complete tra5 transposon harboring orthologs of SAP11, SAP54, and SAP05 effectors indicating an original phytoplasma pathogenicity island. Our results deepen the understanding of phytoplasma evolution and reaffirm the heterogeneity of stolbur phytoplasmas.