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Contents

  1. Introduction: Overview of Fungal Genomics.
  2. Hands-on training in web-based data-mining resources for fungal genomes.
  3. PLOS ONE: Fungal genomics

Genomics of Candida albicans S. Salomon, A. Felk, W. Molecular genetics and genomics of Phytophthora S. Genomics of phytopathogenicFusarium H. Suga, M. Genomics of Fusarium venenatum: An alternative fungal host for making enzymes R. Berka et al. Molecular characterization of Rhizoctonia solani M. Genomics ofTrichoderma M.

Rey et al. Genomics of economically significant Aspergillus and Fusarium species J. Yu et al. Penicillium genomics J. Royer et al. Genomics of Neurospora crassa: From one-gene-one-enzyme to 10, genes E. Braun et al. Genetics and genomics of Mycosphaerella graminicola: A model for the Dothideales S. Goodwin, C. Waalwijk, G. Functional genomic analysis of the rice blast fungusMagnaporthe grisea M.

Gilbert, D. Soanes, N. Genomics of entomopathogenic fungi G. Khachatourians, D. Genomics of arbuscular mycorrhizal fungi N. Ferrol et al. Keyword Index.

Introduction: Overview of Fungal Genomics.

Research in the genomics of a handful of fungi has matured at an unprecedented rate allowing comprehensive review. Developments in fungal genomics should be of great significance to new strategies in fields where disciplinary crossovers of fungal genomics, genes and their regulation, expression, and engineering will have a strong impact in dealing with agriculture, foods, natural resources, life sciences, biotechnology, informatics, metabolomics, pharmaceuticals and bioactive compounds.

This volume analyzes the commonly used molecular markers systems, and elaborates the development of biochemical genetics, which provides a model system that established the relationship between genes and enzymes. Current knowledge about the genomic and genetic variability of Candida albicans, the polymorphic fungus that is an opportunistic human pathogen of increasing medical importance, has been covered in detail.

Current understanding of the genetics and functional genomic analysis of the most important fungal pathogens of staple food crops, rice and wheat among others is covered including chapters dealing with the genomics of economically important fungi such asMagnaporthe grisea, Aspergillus, Fusarium, Penicillium, Trichoderma, Rhizoctonia, Mycosphaerella graminicola, and entomopathogenic fungi. With several thousand recent citations, it is hoped that volume four will serve as a useful reference for knowledgeable veterans and beginners as well as those crossing disciplinary boundaries into the exciting field of biotechnology, genomics and bioinformatics of fungi.

We are always looking for ways to improve customer experience on Elsevier. We would like to ask you for a moment of your time to fill in a short questionnaire, at the end of your visit. If you decide to participate, a new browser tab will open so you can complete the survey after you have completed your visit to this website. Genomes labeled as incomplete are typically parasites, which suggest that gene losses from genome streamlining and missing sequence in assemblies might be confounded.

These results indicate that a different set of representative sequence will be necessary for obligate parasites. To avoid overcounting false positives and inflating the estimate, gene fragment sequences are required to score above a predetermined threshold to be accepted as valid hit. However, because short fragments are still required to display a significant similarity versus FGMP protein markers scores , the likelihood of inflated completeness estimates is expected to be negligible.

Runtimes are more influenced by the level of fragmentation of the assembly than its size Additional file 7. The fastest runtime observed was that of Cryptococcus gattii assembly version 1, size FGMP is a useful tool for automated assessment of genome assembly completeness of fungal genomes that incorporates measures of gene content covering both protein coding and noncoding regions.

Hands-on training in web-based data-mining resources for fungal genomes.

The tool combines multilevel analysis by scanning of both coding and non-coding regions of a given genome and provides a detailed reported describing the recovery of multiple types of genomic features in a genome assembly. FGMP reports complete, partial and aberrant gene models. FGMP also includes an experimental module, which allow a user to query raw reads using a reservoir sampling approach. This module is currently optimized for low input long reads similar to PacBio or Nanopore sequences.

Future versions will include support for estimation from Illumina reads. FGMP has a modular architecture and thus can be easily incorporated into existing genome annotation pipelines. A realistic estimation of level of genome completeness is a critical metric for accurate comparative genomics studies. This is particularly relevant as the sequencing costs decrease and whole genome assembly is attempted as daily routine for many purposes.

PLOS ONE: Fungal genomics

BUSCO is currently the only maintained tool for such purpose. FGMP fills a unique niche in the sense that it has modules that assay additional feature types in genomes with no equivalent in existing methods. The tool allows a deeper analysis in the context of evolutionary biology by quickly providing key metrics such the presence of potentially collapsed regions or can be used to screen reads before computationally costly genome assembly is attempted. FGMP is written in Perl 5, and is designed for a command line interface. Check the status of multi-copy protein families: scans the raw predictions and identify markers that are expected to be in multiple copies.

Markers with a lower number of copies than expected are tagged as potentially collapsed regions. Generate final report: gather all raw predictions, filter aberrant predictions at least twice the average length of the reference makers and choose the longest gene model for each protein markers. Infer genome completeness from long reads: is triggered when reads are provided. The present and future of de novo whole-genome assembly. Brief Bioinform. Insights into the phylogeny and coding potential of microbial dark matter. The human microbiome project. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism.

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.

Nat Genet. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Assessing the gene space in draft genomes. Nucleic Acids Res. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol. BMC Bioinformatics. Stajich JE.

Fungal Genomes and Insights into the Evolution of the Kingdom. Microbiol Spectr. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. Yandell M, Ence D. A beginner's guide to eukaryotic genome annotation. Nat Rev Genet. REAPR: a universal tool for genome assembly evaluation. Genome Biol. QUAST: quality assessment tool for genome assemblies. Bioconda: sustainable and comprehensive software distribution for the life sciences.

Nat Methods. The OMA orthology database in function predictions, better plant support, synteny view and other improvements. Trends Genet. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Slater GS, Birney E.

Automated generation of heuristics for biological sequence comparison. BMC bioinformatics. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

About this book

InterProScan 5: genome-scale protein function classification. Adaptive seeds tame genomic sequence comparison.