An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Abstract

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Keywords: extremophiles; fungi; human opportunistic; lichens; plant pathogens.

Figure 1

Fungi used in genomic studies. (A)Microcolonial black fungus Lichenothelia calcarea (L1799) [94], axenic culture of (B) the polyextremotolerant halophitic black yeast Hortaea werneckii EXF-6566 [91], (C) Knufia chersonesos (MA5789) and (D) Cryomyces antarcticus (MA5682); the lichen species (E) Rhizoplaca melanophthalma [134] and (F) Pseudevernia furfuracea [115]; axenic culture isolate of the lichen forming fungi (mycobiont) (G) Arthonia radiata [Appendix A] and (H) Rhizoplaca melanophthalma [136]. Photos (A,B,E,G,H) by Lucia Muggia, (C) by Donatella Tesei, (D) by Christian Voitl, (F) by Heinrich Meier. Scale bars: (A) 0.5 mm, (B) 1 mm, (C–E) 2 cm, (F) 5 cm, (G,E) 5 mm, (H) 1 cm.

Figure 2

Ascomycota tree of life. Topology, sub-phyla and classes included are taken from Spatafora et al. (2017). Next to each taxa is reported the number of assemblies retrieved from NCBI database (6 July 2020). For the five most diverse classes in Ascomycota also orders that have at least one genome sequenced are reported; bar charts are in percentage. Data were retrieved from NCBI assembly reports, using the ncbi-genome-download script (https://github.com/kblin/ncbi-genome-download/) [148] and a custom script which exploits NCBI Entrez Programming Utilities to retrieve taxonomy.

Figure 3

Most used assembly methods by year expressed in percentage. Data were retrieved from NCBI assembly reports, using the ncbi-genome-download script (https://github.com/kblin/ncbi-genome-download/) [148] and a custom script which exploits NCBI Entrez Programming Utilities to retrieve taxonomy. Data for 2020 are only present for assemblies submitted by July 2020. Only tools used for 35 or more genome assemblies are reported. The following tools are not included: SSPACE, SMRT, PILON, SMART, GS, Custom, Gapfiller, Ragout, PCAP, MEGAHIT, Geneious, RaGOO, Phrap, DBG2OLC, Arachne, Roche gs, Albacore, Redundans, HBAR, Minimap, Unicycler, Flye, SeqMan, DNASTAR, MECAT, Casava, Edena, HABOT, Hybrid, Jazz, PBcR, PBJerry, Quiver.

Figure 4

General workflow for fungal proteomics. Steps from cultivation to bioinformatic analysis are shown, with a focus on the three main sample types: (A) whole-cell proteome, (B) extracellular proteins (secretome) and (C) membrane and cell-wall associated proteins. The image was created with BioRender.com.