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Advances in Genomics of Human Fungal Pathogens

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Population Genomics: Microorganisms

Part of the book series: Population Genomics ((POGE))

Abstract

Fungi are responsible for 1.5 million deaths every year, and one-third of the human population has experienced a fungal infection. The increasing numbers of immunocompromised people are associated with the increased incidence of human mycosis, either from medical interventions such as cancer therapy or transplantation or due to other underlying diseases such as HIV/AIDS or diabetes. Additionally, climate change has been implicated in widening distributions of endemic fungi, potentially expanding beyond previously restricted ranges. In this chapter, we will address two main classes of fungal pathogens: first, the globally distributed fungi such as Candida, Aspergillus, and Cryptococcus, followed by a discussion of endemic fungal pathogens and their relatives Paracoccidioides, Histoplasma, Coccidioides, and Emmonsia. In the past, virulence and pathogenesis studies were limited to few infection models and biomarkers, but these studies have progressed significantly with the advances of DNA sequencing and genetic tools. Newly sequenced structural (DNA) and functional (RNA and protein) genomes provide a scaffold to understand gene gain and loss that might be associated with mammalian infection and disease progression. During infection, these pathogens express a wide range of genes that are associated with either establishment of infection or escaping recognition by host immune cells. Moreover, population genomic studies reveal that pathogen complexes exhibit different strategies to generate genetic diversity either via sexual or parasexual recombination, and this phenomenon may be implicated in altered virulence, disease presentation, and antifungal resistance. The literature of genomic studies of the abovementioned pathogenic fungal genera are summarized, and molecular taxonomy and population structure are explored, as well as a survey of the main genomic characteristics, chromosomal variation, gene content, and expression. Comparative genomics between pathogenic and nonpathogenic close-related species provides evidence of both convergent and unique adaptation of those fungal lineages to mammalian hosts. A better understanding of patterns of gene flow among species (hybridization), adaptation and evolutionary potential, fully closed reference genomes, and general improvement of gene annotation and function is needed.

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Authors and Affiliations

  1. The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA

    Daniel Raymond Kollath, Marcus de Melo Teixeira & Bridget Marie Barker

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  1. Daniel Raymond Kollath
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  2. Marcus de Melo Teixeira
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  1. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Martin F. Polz

  2. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada

    Om P. Rajora

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Kollath, D.R., de Melo Teixeira, M., Barker, B.M. (2018). Advances in Genomics of Human Fungal Pathogens. In: Polz, M., Rajora, O. (eds) Population Genomics: Microorganisms. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_41

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