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  1. Article ; Online: Genome biology and evolution of mating-type loci in four cereal rust fungi.

    Luo, Zhenyan / McTaggart, Alistair / Schwessinger, Benjamin

    PLoS genetics

    2024  Volume 20, Issue 3, Page(s) e1011207

    Abstract: Permanent heterozygous loci, such as sex- or mating-compatibility regions, often display suppression of recombination and signals of genomic degeneration. In Basidiomycota, two distinct loci confer mating compatibility. These loci encode homeodomain (HD) ...

    Abstract Permanent heterozygous loci, such as sex- or mating-compatibility regions, often display suppression of recombination and signals of genomic degeneration. In Basidiomycota, two distinct loci confer mating compatibility. These loci encode homeodomain (HD) transcription factors and pheromone receptor (Pra)-ligand allele pairs. To date, an analysis of genome level mating-type (MAT) loci is lacking for obligate biotrophic basidiomycetes in the Pucciniales, an order containing serious agricultural plant pathogens. Here, we focus on four species of Puccinia that infect oat and wheat, including P. coronata f. sp. avenae, P. graminis f. sp. tritici, P. triticina and P. striiformis f. sp. tritici. MAT loci are located on two separate chromosomes supporting previous hypotheses of a tetrapolar mating compatibility system in the Pucciniales. The HD genes are multiallelic in all four species while the PR locus appears biallelic, except for P. graminis f. sp. tritici, which potentially has multiple alleles. HD loci are largely conserved in their macrosynteny, both within and between species, without strong signals of recombination suppression. Regions proximal to the PR locus, however, displayed signs of recombination suppression and genomic degeneration in the three species with a biallelic PR locus. Our observations support a link between recombination suppression, genomic degeneration, and allele diversity of MAT loci that is consistent with recent mathematical modelling and simulations. Finally, we confirm that MAT genes are expressed during the asexual infection cycle, and we propose that this may support regulating nuclear maintenance and pairing during infection and spore formation. Our study provides insights into the evolution of MAT loci of key pathogenic Puccinia species. Understanding mating compatibility can help predict possible combinations of nuclear pairs, generated by sexual reproduction or somatic recombination, and the potential evolution of new virulent isolates of these important plant pathogens.
    MeSH term(s) Edible Grain/genetics ; Basidiomycota/genetics ; Genomics ; Genome, Fungal/genetics ; Reproduction ; Plant Diseases/genetics ; Plant Diseases/microbiology
    Language English
    Publishing date 2024-03-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1011207
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  2. Article: Whole-mitochondrial genomes of

    Powell, Daniel / Schwessinger, Benjamin / Frère, Céline H

    Ecology and evolution

    2023  Volume 13, Issue 3, Page(s) e9955

    Abstract: Infectious fungal diseases can have devastating effects on wildlife health and a detailed understanding of the evolution of related emerging fungal pathogen along with the ability to detect them in the wild is considered indispensable for effective ... ...

    Abstract Infectious fungal diseases can have devastating effects on wildlife health and a detailed understanding of the evolution of related emerging fungal pathogen along with the ability to detect them in the wild is considered indispensable for effective management strategies. Several fungi from the genera
    Language English
    Publishing date 2023-03-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2635675-2
    ISSN 2045-7758
    ISSN 2045-7758
    DOI 10.1002/ece3.9955
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  3. Article ; Online: Fundamental wheat stripe rust research in the 21

    Schwessinger, Benjamin

    The New phytologist

    2016  Volume 213, Issue 4, Page(s) 1625–1631

    Abstract: Contents 1625 I. 1625 II. 1626 III. 1626 IV. 1626 V. 1628 VI. 1629 VII. 1629 1630 References 1630 SUMMARY: In the ... ...

    Abstract Contents 1625 I. 1625 II. 1626 III. 1626 IV. 1626 V. 1628 VI. 1629 VII. 1629 1630 References 1630 SUMMARY: In the 21
    MeSH term(s) Adaptation, Physiological ; Basidiomycota/genetics ; Basidiomycota/physiology ; Genetic Variation ; History, 21st Century ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Research/history ; Triticum/microbiology
    Language English
    Publishing date 2016-08-30
    Publishing country England
    Document type Historical Article ; Journal Article ; Review
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.14159
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    Z 868: Show issues

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  4. Article ; Online: Plant genome evolution in the genus

    Ferguson, Scott / Jones, Ashley / Murray, Kevin / Andrew, Rose / Schwessinger, Benjamin / Borevitz, Justin

    Genome research

    2024  Volume 34, Issue 4, Page(s) 606–619

    Abstract: Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to ... ...

    Abstract Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving
    MeSH term(s) Eucalyptus/genetics ; Genome, Plant ; Evolution, Molecular ; Synteny ; Gene Rearrangement ; Phylogeny ; Chromosomes, Plant/genetics ; Genetic Variation
    Language English
    Publishing date 2024-05-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.277999.123
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3729: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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  5. Article ; Online: Editorial overview: Biotic interactions - from single molecules to complex ecosystems.

    Schwessinger, Benjamin / Krasileva, Ksenia V

    Current opinion in plant biology

    2020  Volume 56, Page(s) A1–A4

    Language English
    Publishing date 2020-07-17
    Publishing country England
    Document type Editorial
    ZDB-ID 1418472-2
    ISSN 1879-0356 ; 1369-5266
    ISSN (online) 1879-0356
    ISSN 1369-5266
    DOI 10.1016/j.pbi.2020.06.004
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    In stock of ZB MED Bonn / Germany

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  6. Article: Fundamental wheat stripe rust research in the 21st century

    Schwessinger, Benjamin

    new phytologist. 2017 Mar., v. 213, no. 4

    2017  

    Abstract: Contents 1625 I. 1625 II. 1626 III. 1626 IV. 1626 V. 1628 VI. 1629 VII. 1629 1630 References 1630 SUMMARY: In the 21ˢᵗ century, the wheat stripe rust fungus has evolved to be the largest biotic limitation to global wheat production. New pathogen ... ...

    Abstract Contents 1625 I. 1625 II. 1626 III. 1626 IV. 1626 V. 1628 VI. 1629 VII. 1629 1630 References 1630 SUMMARY: In the 21ˢᵗ century, the wheat stripe rust fungus has evolved to be the largest biotic limitation to global wheat production. New pathogen genotypes are more aggressive and able to infect previously resistant wheat varieties, leading to rapid pathogen migration across and between continents. We now know the full life cycle, microevolutionary relationships and past migration routes on a global scale. Current sequencing technologies have provided the first fungal draft genomes and simplified plant resistance gene cloning. Yet, we know nothing about the molecular and microevolutionary mechanisms that facilitate the infection process and cause new devastating pathogen races. These are the questions that need to be addressed by exploiting the synergies between novel 21ˢᵗ century biology tools and decades of dedicated pathology work.
    Keywords crop production ; genetic resistance ; genome ; genotype ; molecular cloning ; plant pathogenic fungi ; races ; stripe rust ; wheat
    Language English
    Dates of publication 2017-03
    Size p. 1625-1631.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note REVIEW
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.14159
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    In stock of ZB MED Bonn / Germany

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  7. Article ; Online: Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus

    Ferguson, Scott / Jones, A. P. / Murray, Kevin / Schwessinger, Benjamin / Borevitz, Justin O.

    Molecular Ecology. 2023 Mar., v. 32, no. 6 p.1271-1287

    2023  

    Abstract: Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely ... ...

    Abstract Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long‐read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small‐scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species.
    Keywords DNA ; Eucalyptus ; ecology ; genetic variation ; genome ; homologous recombination ; progeny ; transposons
    Language English
    Dates of publication 2023-03
    Size p. 1271-1287.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.16608
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  8. Article ; Online: Cost-conscious generation of multiplexed short-read DNA libraries for whole-genome sequencing.

    Jones, Ashley / Stanley, David / Ferguson, Scott / Schwessinger, Benjamin / Borevitz, Justin / Warthmann, Norman

    PloS one

    2023  Volume 18, Issue 1, Page(s) e0280004

    Abstract: Massively parallel, second-generation short-read DNA sequencing has become an integral tool in biology for genomic studies. Offering highly accurate base-pair resolution at the most competitive price, the technology has become widespread. However, high- ... ...

    Abstract Massively parallel, second-generation short-read DNA sequencing has become an integral tool in biology for genomic studies. Offering highly accurate base-pair resolution at the most competitive price, the technology has become widespread. However, high-throughput generation of multiplexed DNA libraries can be costly and cumbersome. Here, we present a cost-conscious protocol for generating multiplexed short-read DNA libraries using a bead-linked transposome from Illumina. We prepare libraries in high-throughput with small reaction volumes that use 1/50th the amount of transposome compared to Illumina DNA Prep tagmentation protocols. By reducing transposome usage and optimising the protocol to circumvent magnetic bead-based clean-ups between steps, we reduce costs, labour time and DNA input requirements. Developing our own dual index primers further reduced costs and enables up to nine 96-well microplate combinations. This facilitates efficient usage of large-scale sequencing platforms, such as the Illumina NovaSeq 6000, which offers up to three terabases of sequencing per S4 flow cell. The protocol presented substantially reduces the cost per library by approximately 1/20th compared to conventional Illumina methods.
    MeSH term(s) Gene Library ; DNA/genetics ; Sequence Analysis, DNA/methods ; Genome ; Genomics ; High-Throughput Nucleotide Sequencing/methods
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-01-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0280004
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  9. Article: Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections.

    Hoang, Minh Thuy Vi / Irinyi, Laszlo / Hu, Yiheng / Schwessinger, Benjamin / Meyer, Wieland

    Frontiers in microbiology

    2022  Volume 12, Page(s) 708550

    Abstract: Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on ... ...

    Abstract Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent
    Language English
    Publishing date 2022-01-06
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.708550
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  10. Article ; Online: Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus.

    Ferguson, Scott / Jones, Ashley / Murray, Kevin / Schwessinger, Benjamin / Borevitz, Justin O

    Molecular ecology

    2022  Volume 32, Issue 6, Page(s) 1271–1287

    Abstract: Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely ... ...

    Abstract Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long-read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small-scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species.
    MeSH term(s) Eucalyptus/genetics ; Genome ; Synteny/genetics ; Chromosomes ; Sequence Analysis, DNA/methods
    Language English
    Publishing date 2022-07-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.16608
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    In stock of ZB MED Bonn / Germany

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