Advancement of Functional Genomics of a Model Species of Neurospora and Its Use for Ecological Genomics of Soil Fungi

Lee, Kwangwon; Dighton, John

doi:10.1007/978-3-642-39339-6_3

Cited by 4 publications

(2 citation statements)

References 103 publications

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“…The use of gene knock-outs in combination with transcriptomics could provide a transition from model organisms into the 'real world' system (Lee and Dighton 2013 ). However, Nehr ( 2010 ) has shown that molecular primers developed for the model nematode Caenorhabditis elegans do not work with a number of groups of soil dwelling bactiverous nematodes, so the translation of information from model organisms to similar groups in the natural world may not be as simple as thought.…”

Section: New Tools In the Tool Box: Molecular Determination Of Diversmentioning

confidence: 99%

Introduction: Soils and Their Promotion of Plant Growth

Dighton

2014

Interactions in Soil: Promoting Plant Growth

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Soil is a complex milieu of physical and biological entities that regulates the availability of nutrients for plant growth. The interactions between the elements of the soil biota and the plants during this process are complex and often rely on feedbacks between the plants and the great diversity of soil organisms that function to regulate processes to support plant growth. The rhizosphere and its mycorrhizal component are important parts of the connection between the plant and soil through its roots. This zone is a 'hot-spot' of microbial activity and trophic interactions with other soil organisms. It is here that growth of the plant root is infl uenced by nutrient availability, induction of root growth stimulating auxins, the interaction with plant pathogens and herbivores. Ecosystem engineers in the form of earthworms and other burrowing fauna are important in altering both the physical structure of soil and rates of decomposition of organic residues. A little researched component of soil is viruses. Their interaction with microbial and faunal communities is introduced here. Many of the soil processes infl uencing plant growth and the diversity of soil organisms is infl uenced by human activities ranging from agricultural and forestry practices through urbanization to the infl uence of pollution from industrial processes. To help us with the understanding of the interactions between biodiversity and function, new molecular tools involving metagenomics and transcriptomics are evolving, and are discussed here as an emerging suite of tools that can be applied to soil ecology. The chapter introduces the detail to come in subsequent chapters of this book.

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Section: New Tools In the Tool Box: Molecular Determination Of Diversmentioning

confidence: 99%

Introduction: Soils and Their Promotion of Plant Growth

Dighton

2014

Interactions in Soil: Promoting Plant Growth

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“…As the first step toward this goal, Neurospora has been grown on different natural substrata (Lee, 2012). Utilizing new functional genomics tools, Neurospora could serve as a model system for addressing circadian-clock associated ecological questions (Ellison et al, 2011; Lee, 2012; Lee & Dighton, 2013; Romero-Olivares, Taylor, & Treseder, 2015)…”

Section: Natural Variation and The Circadian Clockmentioning

confidence: 99%

Natural Variation of the Circadian Clock in Neurospora

Koritala

Lee

2017

Natural Variation and Clocks

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Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.

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Current trends, limitations and future research in the fungi?

Hyde,

Baldrian,

Chen

et al. 2024

Fungal Diversity

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The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing limitations, and suggests future areas where scientists can focus their efforts, in the field mycology. We show how fungi have become important emerging diseases in medical mycology. We discuss current trends and the potential of fungi in drug and novel compound discovery. We explore the current trends in phylogenomics, its potential, and outcomes and address the question of how phylogenomics can be applied in fungal ecology. In addition, the trends in functional genomics studies of fungi are discussed with their importance in unravelling the intricate mechanisms underlying fungal behaviour, interactions, and adaptations, paving the way for a comprehensive understanding of fungal biology. We look at the current research in building materials, how they can be used as carbon sinks, and how fungi can be used in biocircular economies. The numbers of fungi have always been of great interest and have often been written about and estimates have varied greatly. Thus, we discuss current trends and future research needs in order to obtain more reliable estimates. We address the aspects of machine learning (AI) and how it can be used in mycological research. Plant pathogens are affecting food production systems on a global scale, and as such, we look at the current trends and future research needed in this area, particularly in disease detection. We look at the latest data from High Throughput Sequencing studies and question if we are still gaining new knowledge at the same rate as before. A review of current trends in nanotechnology is provided and its future potential is addressed. The importance of Arbuscular Mycorrhizal Fungi is addressed and future trends are acknowledged. Fungal databases are becoming more and more important, and we therefore provide a review of the current major databases. Edible and medicinal fungi have a huge potential as food and medicines, especially in Asia and their prospects are discussed. Lifestyle changes in fungi (e.g., from endophytes, to pathogens, and/or saprobes) are also extremely important and a current research trend and are therefore addressed in this special issue of Fungal Diversity.

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Advancement of Functional Genomics of a Model Species of Neurospora and Its Use for Ecological Genomics of Soil Fungi

Cited by 4 publications

References 103 publications

Introduction: Soils and Their Promotion of Plant Growth

Introduction: Soils and Their Promotion of Plant Growth

Natural Variation of the Circadian Clock in Neurospora

Current trends, limitations and future research in the fungi?

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