scholarly journals Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defences

2020 ◽  
Author(s):  
Cécile Lorrain ◽  
Alice Feurtey ◽  
Mareike Möller ◽  
Janine Haueisen ◽  
Eva Stukenbrock
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Related Species ◽  
Plant Pathogens ◽  
De Novo ◽  
Zymoseptoria Tritici ◽  
Closely Related Species ◽  
Fungal Plant Pathogens ◽  
Wide Range ◽  
The Impact

AbstractTransposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires, suggesting variation in the efficacy of genome defences. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in thirteen genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The thirteen genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with distinct genome compartments in all Zymoseptoria species, including chromosomal rearrangements, genes showing presence/absence variation and effectors. European Z. tritici isolates have reduced signatures of Repeat-Induced Point mutations compared to Iranian isolates and closely related species. Our study supports the hypothesis that ongoing but moderate TE mobility in Zymoseptoria species shapes pathogen genome evolution.

scholarly journals Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Cécile Lorrain ◽  
Alice Feurtey ◽  
Mareike Möller ◽  
Janine Haueisen ◽  
Eva Stukenbrock
Keyword(s):  
Transposable Elements ◽  
Related Species ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
De Novo ◽  
Zymoseptoria Tritici ◽  
Closely Related Species ◽  
Fungal Plant Pathogens ◽  
Wide Range ◽  
The Impact

Abstract Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.

scholarly journals Fusarium: a ubiquitous fungus of global significance

2012 ◽  
Vol 33 (1) ◽  
pp. 22 ◽  
Author(s):  
LW Burgess ◽  
WL Bryden
Keyword(s):  
Plant Pathogens ◽  
Disease Incidence ◽  
Farming Systems ◽  
Plant Diseases ◽  
Natural Ecosystems ◽  
Fungal Plant Pathogens ◽  
Wide Range ◽  
Socio Economic Impact ◽  
Key Aspects ◽  
The Impact

Fusarium is one of the most economically important genera of fungal plant pathogens, causing significant crop losses and contamination of grain by mycotoxins on a global basis. Some species also cause infections (mycoses) of humans and other animals. Fusarium includes many species, a significant number of which cause a wide range of plant diseases that affect many crops including major food and fibre crops such as wheat, barley, maize, bananas and cotton, often with devastating socio-economic impact. The diseases are often insidious and extremely difficult to control. Its success as a plant pathogen can be attributed to wide host ranges, endophytic infection, and varied modes of survival and dispersal. Representatives occur in virtually all bioclimatic regions of the world in agricultural and natural ecosystems. In this article we present a summary of the key aspects of the biology and morphology of Fusarium and then briefly discuss several plant diseases to illustrate the diverse nature and devastating effects of these fungi, their mycotoxins, the impact of no-till farming systems on disease incidence, and the poorly understood but key role of endophytic colonisation in the disease cycle. Inevitably, the coverage is selective but it indicates the potential global impact of this fungal genus on plant disease and food security.

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

Revision of Coronostrongylus (Nematoda : Strongyloidea) parasitic in the stomachs of macropodid marsupials

2002 ◽  
Vol 16 (6) ◽  
pp. 893 ◽  
Author(s):  
I. Beveridge
Keyword(s):  
Papua New Guinea ◽  
Host Species ◽  
Related Species ◽  
New Guinea ◽  
Nematode Species ◽  
Closely Related Species ◽  
Nematode Genus ◽  
Eastern Australia ◽  
Wide Range ◽  
Species Occurrences

The monotypic nematode genus Coronostrongylus Johnston & Mawson, 1939 from the stomachs of macropodid marsupials was reviewed and was found to consist of a least seven closely related species. Coronostrongylus coronatus Johnston & Mawson, 1939 is found most commonly in Macropus rufogriseus, but occurs occasionally in M. dorsalis, M. parryi and Petrogale inornata. Coronostrongylus johnsoni, sp. nov. is most commonly found in M. dorsalis, but occurs also in M. rufogriseus, M. parma, Thylogale stigmatica, Petrogale godmani and P. brachyotis. Coronostrongylus barkeri, sp. nov. is most prevalent in Onychogalea unguifera, but occurs also in M. rufus, M. robustus and P. brachyotis. Coronostrongylus closei, sp. nov. is restricted to Petrogale persephone. Coronostrongylus sharmani, sp. nov. occurs only in rock wallabies from eastern Australia: P.�coenensis, P. godmani and P. mareeba; C. spratti, sp. nov. occurs in P. inornata and P. assimilis. Coronostrongylus spearei, sp. nov. is restricted to Papua New Guinea where it is found in Dorcopsulus vanhearni, Dorcopsis hageni and D. muelleri. Although all of the nematode species occur in one principal host species or a series of closely related host species, occurrences in geographically disjunct areas and in phylogenetically distant hosts are features of C. coronatus, C. barkeri, sp. nov. and C. johnsoni, sp. nov. The occurrence of seven closely related nematode species found in a wide range of macropodid host species is more readily accounted for by a hypothesis involving multiple colonisations of hosts than by the hypothesis of co-speciation.

scholarly journals Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

2021 ◽  
Author(s):  
Ching-Ho Chang ◽  
Lauren E. Gregory ◽  
Kathleen E. Gordon ◽  
Colin D. Meiklejohn ◽  
Amanda M. Larracuente
Keyword(s):  
Positive Selection ◽  
Y Chromosome ◽  
Related Species ◽  
De Novo ◽  
Gene Families ◽  
Chromosome Organization ◽  
End Joining ◽  
Sexual Antagonism ◽  
Closely Related Species ◽  
Y Chromosomes

AbstractY chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposable elements, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization.

scholarly journals Software Evaluation for de novo Detection of Transposons

2021 ◽  
Author(s):  
Matias Rodriguez ◽  
Wojciech Makałowski
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Simulated Data ◽  
Genomic Sequences ◽  
Software Evaluation ◽  
Easy Task ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

Genome Evolution of Fungal Plant Pathogens

2021 ◽  
Author(s):  
Maria Aragona ◽  
Alessandro Infantino ◽  
Maria Teresa Valente ◽  
Alessandro Grottoli ◽  
Anita Haegi
Keyword(s):  
Genome Evolution ◽  
Plant Pathogens ◽  
Fungal Plant Pathogens

scholarly journals Transposable Elements and the Evolution of Insects

2021 ◽  
Vol 66 (1) ◽  
pp. 355-372
Author(s):  
Clément Gilbert ◽  
Jean Peccoud ◽  
Richard Cordaux
Keyword(s):  
Transposable Elements ◽  
Related Species ◽  
Horizontal Transfer ◽  
Population Genomics ◽  
Antiviral Immunity ◽  
Closely Related Species ◽  
Phylogenetic Relatedness ◽  
Functional Studies ◽  
Insect Symbionts

Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.

Effects of elevated pCO2 on crab survival and exoskeleton composition depend on shell function and species distribution: a comparative analysis of carapace and claw mineralogy across four porcelain crab species from different habitats

2016 ◽  
Vol 74 (4) ◽  
pp. 1021-1032 ◽  
Author(s):  
Tessa M. Page ◽  
Samantha Worthington ◽  
Piero Calosi ◽  
Jonathon H. Stillman
Keyword(s):  
Related Species ◽  
Intertidal Zone ◽  
Divalent Cations ◽  
Elevated Pco2 ◽  
Physiological Adaptation ◽  
Elevated Concentration ◽  
Cation Composition ◽  
Closely Related Species ◽  
Intertidal Species ◽  
The Impact

Elevated concentration of carbon dioxide (elevated pCO2) that cause reduced pH is known to influence calcification in many marine taxa, but how elevated pCO2 influences cation composition of mineralized structures is less well studied. To a large extent, the degree to which elevated pCO2 impacts mineralized structures is influenced by physiological adaptation of organisms to environments where low pH is routinely experienced. Here, we test the hypotheses that elevated pCO2 will differently impact the relative concentrations of divalent cations (Ca2+, Mg2+, Sr2+, and Mn2+) in four closely related species of porcelain crabs distributed across intertidal zone gradients. Cation composition of carapace and claw exoskeleton was determined using inductively coupled plasma mass spectrometry following 24-day exposures to pH/pCO2 levels of 8.0/418 and 7.4/1850 µatm during the intermoult period. Reduced pH/elevated pCO2 caused a 13–24% decrease of carapace [Ca2+] across all species, and species-specific responses in carapace and claw [Mg2+], [Sr2+] and [Mn2+] were observed. During a 24-day exposure, reduced pH/elevated pCO2 reduced survival probability in low-intertidal but not mid-intertidal species. Overall, the effect of reduced pH/elevated pCO2 on exoskeleton mineral composition was muted in mid-intertidal species relative to low-intertidal species, indicating that extant adaptation to the variable intertidal zone may lessen the impact of ocean acidification (OA) on maintenance of mineralized structures. Differences in responses to reduced pH/elevated pCO2 among closely related species adds complexity to predictive inferences regarding the effects of OA.

Are polymorphic species of Uropodina (Acari: Mesostigmata) more successful evolutionarily?—A case study of closely related species from the genus Oodinychus Berlese, 1917 based on DNA sequences

2019 ◽  
Vol 24 (5) ◽  
pp. 866
Author(s):  
Jerzy Błoszyk ◽  
Katarzyna Buczkowska ◽  
Anna Maria Bobowicz ◽  
Alina Bączkiewicz ◽  
Zbigniew Adamski ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Habitat Preferences ◽  
Abundant Species ◽  
Systematic Position ◽  
Genetic Differences ◽  
Similar Species ◽  
Closely Related Species ◽  
Wide Range

The study presented in this research paper is the first taxonomic investigation focusing on Uropodina (Acari: Mesostigmata) mites with a brief discussion of the genetic differences of two very closely related species from the genus Oodinychus Berlese, 1917, i.e. O. ovalis (C.L. Koch, 1839) and O. karawaiewi (Berlese, 1903). These two morphologically similar species are quite common and they have a wide range of occurrence in Europe. They also live in almost the same types of habitat. However, O. ovalis usually exhibits higher abundance and frequency of occurrence. The major aim of the study was to carry out a comparative analysis of the systematic position, morphological and biological differences, as well as habitat preferences and distribution of O. ovalis and O. karawaiewi. The next aim was to ascertain whether the differences in number and frequency of these species may stem from the genetic differences at the molecular level (16S rDNA and COI). The study shows that O. ovalis, which is a more abundant species than O. karawaiewi, turned out to be genetically more polymorphic.

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