Approaches for Comparative Genomics in Aspergillus and Penicillium

Jane Lind Nybo Rasmussen, Sebastian Theobald, Julian Brandl, Tammi Camilla Vesth, Mikael Rørdam Andersen

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

    Abstract

    The number of available genomes in the closely related fungal genera Aspergillus and Penicillium is rapidly increasing. At the time of writing, the genomes of 62 species are available, and an even higher number is being prepared. Fungal comparative genomics is thus becoming steadily more powerful and applicable for many types of studies. In this chapter, we provide an overview of the state-of-the-art of comparative genomics in these fungi, along with recommended methods. The chapter describes databases for fungal comparative genomics. Based on experience, we suggest strategies for multiple types of comparative genomics, ranging from analysis of single genes, over gene clusters and CaZymes to genome-scale comparative genomics. Furthermore, we have examined published comparative genomics papers to summarize the preferred bioinformatic methods and parameters for a given type of analysis, highly useful for new fungal geneticists. Moreover, the chapter contains a detailed overview of comparative genomics studies of key fungal traits such as primary metabolism, secondary metabolism, and secretome analysis. Finally, we gaze into a possible future of the field by comparing the current state of fungal comparative genomics to the development in bacterial genomics, where the comparison of hundreds of genomes has been performed for a while.
    Original languageEnglish
    Title of host publicationAspergillus and Penicillium in the Post-genomic Era
    Editors Ronald P. de Vries, Isabelle Benoit Gelber, Mikael Rørdam Andersen
    PublisherCaister Academic Press
    Publication date2016
    Chapter4
    ISBN (Print)978-1-910190-39-5
    ISBN (Electronic)978-1-910190-40-1
    Publication statusPublished - 2016

    Cite this

    Rasmussen, J. L. N., Theobald, S., Brandl, J., Vesth, T. C., & Andersen, M. R. (2016). Approaches for Comparative Genomics in Aspergillus and Penicillium. In R. P. de Vries, I. Benoit Gelber, & M. Rørdam Andersen (Eds.), Aspergillus and Penicillium in the Post-genomic Era Caister Academic Press.
    Rasmussen, Jane Lind Nybo ; Theobald, Sebastian ; Brandl, Julian ; Vesth, Tammi Camilla ; Andersen, Mikael Rørdam. / Approaches for Comparative Genomics in Aspergillus and Penicillium. Aspergillus and Penicillium in the Post-genomic Era. editor / Ronald P. de Vries ; Isabelle Benoit Gelber ; Mikael Rørdam Andersen. Caister Academic Press, 2016.
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    abstract = "The number of available genomes in the closely related fungal genera Aspergillus and Penicillium is rapidly increasing. At the time of writing, the genomes of 62 species are available, and an even higher number is being prepared. Fungal comparative genomics is thus becoming steadily more powerful and applicable for many types of studies. In this chapter, we provide an overview of the state-of-the-art of comparative genomics in these fungi, along with recommended methods. The chapter describes databases for fungal comparative genomics. Based on experience, we suggest strategies for multiple types of comparative genomics, ranging from analysis of single genes, over gene clusters and CaZymes to genome-scale comparative genomics. Furthermore, we have examined published comparative genomics papers to summarize the preferred bioinformatic methods and parameters for a given type of analysis, highly useful for new fungal geneticists. Moreover, the chapter contains a detailed overview of comparative genomics studies of key fungal traits such as primary metabolism, secondary metabolism, and secretome analysis. Finally, we gaze into a possible future of the field by comparing the current state of fungal comparative genomics to the development in bacterial genomics, where the comparison of hundreds of genomes has been performed for a while.",
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    Rasmussen, JLN, Theobald, S, Brandl, J, Vesth, TC & Andersen, MR 2016, Approaches for Comparative Genomics in Aspergillus and Penicillium. in RP de Vries, I Benoit Gelber & M Rørdam Andersen (eds), Aspergillus and Penicillium in the Post-genomic Era. Caister Academic Press.

    Approaches for Comparative Genomics in Aspergillus and Penicillium. / Rasmussen, Jane Lind Nybo; Theobald, Sebastian; Brandl, Julian; Vesth, Tammi Camilla; Andersen, Mikael Rørdam.

    Aspergillus and Penicillium in the Post-genomic Era. ed. / Ronald P. de Vries; Isabelle Benoit Gelber; Mikael Rørdam Andersen. Caister Academic Press, 2016.

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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    T1 - Approaches for Comparative Genomics in Aspergillus and Penicillium

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    AU - Theobald, Sebastian

    AU - Brandl, Julian

    AU - Vesth, Tammi Camilla

    AU - Andersen, Mikael Rørdam

    PY - 2016

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    N2 - The number of available genomes in the closely related fungal genera Aspergillus and Penicillium is rapidly increasing. At the time of writing, the genomes of 62 species are available, and an even higher number is being prepared. Fungal comparative genomics is thus becoming steadily more powerful and applicable for many types of studies. In this chapter, we provide an overview of the state-of-the-art of comparative genomics in these fungi, along with recommended methods. The chapter describes databases for fungal comparative genomics. Based on experience, we suggest strategies for multiple types of comparative genomics, ranging from analysis of single genes, over gene clusters and CaZymes to genome-scale comparative genomics. Furthermore, we have examined published comparative genomics papers to summarize the preferred bioinformatic methods and parameters for a given type of analysis, highly useful for new fungal geneticists. Moreover, the chapter contains a detailed overview of comparative genomics studies of key fungal traits such as primary metabolism, secondary metabolism, and secretome analysis. Finally, we gaze into a possible future of the field by comparing the current state of fungal comparative genomics to the development in bacterial genomics, where the comparison of hundreds of genomes has been performed for a while.

    AB - The number of available genomes in the closely related fungal genera Aspergillus and Penicillium is rapidly increasing. At the time of writing, the genomes of 62 species are available, and an even higher number is being prepared. Fungal comparative genomics is thus becoming steadily more powerful and applicable for many types of studies. In this chapter, we provide an overview of the state-of-the-art of comparative genomics in these fungi, along with recommended methods. The chapter describes databases for fungal comparative genomics. Based on experience, we suggest strategies for multiple types of comparative genomics, ranging from analysis of single genes, over gene clusters and CaZymes to genome-scale comparative genomics. Furthermore, we have examined published comparative genomics papers to summarize the preferred bioinformatic methods and parameters for a given type of analysis, highly useful for new fungal geneticists. Moreover, the chapter contains a detailed overview of comparative genomics studies of key fungal traits such as primary metabolism, secondary metabolism, and secretome analysis. Finally, we gaze into a possible future of the field by comparing the current state of fungal comparative genomics to the development in bacterial genomics, where the comparison of hundreds of genomes has been performed for a while.

    M3 - Book chapter

    SN - 978-1-910190-39-5

    BT - Aspergillus and Penicillium in the Post-genomic Era

    A2 - de Vries, Ronald P.

    A2 - Benoit Gelber, Isabelle

    A2 - Rørdam Andersen, Mikael

    PB - Caister Academic Press

    ER -

    Rasmussen JLN, Theobald S, Brandl J, Vesth TC, Andersen MR. Approaches for Comparative Genomics in Aspergillus and Penicillium. In de Vries RP, Benoit Gelber I, Rørdam Andersen M, editors, Aspergillus and Penicillium in the Post-genomic Era. Caister Academic Press. 2016