Advances in botanical research. Volume seventy, Fungi / volume editor, Francis M. Martin ; Guus Bakkeren [and forty two others], contributors.

London : Academic Press, 2014.
Advances in Botanical Research, 0065-2296 ; Volume 70
1 online resource (501 p.)
Electronic books.
Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Currently in its 70th volume, the series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on fungi, including pathogenic fungi, symbiotic fungi, saprotrophic fungi and population genomics.Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciencesFeatures a wide range of reviews by
Front Cover; Fungi; Copyright; Contents; Contributors; Preface; Fungal-Plant Interactions: A Never Ending Story of Friends and Foes; Acknowledgement; References; Chapter One: Fungal Genomics: Sequencing and Annotation; 1. Introduction; 2. What Is Genome Assembly, and How to Do It; 2.1. Purpose of assembly; 2.2. Challenges of assembly; 2.3. Sequencing platforms; 2.4. Assembly strategy and algorithms; 2.5. Computational limitations on algorithm choice; 2.6. Paired reads; 2.7. Generation of contigs and scaffolds; 2.8. Assembly quality evaluation; 3. What Is Annotation, and Why Do It
3.1. The purpose of annotation3.2. How to annotate; Gather inputs; Structural annotation; Functional annotation; Distribute outputs; 3.2.1 Assessing and preparing the assembly; 3.2.2. Finding the genes (structural annotation); 3.2.3. Characterizing the genes (functional annotation); 3.2.4. Using and distributing the annotation; 4. What to Do with the Annotation Once You ́ve Got It; 4.1. Comparing the annotation to itself: Duplications and higher-order structure; 4.2. Comparing the annotation with experimental data: other -omics; 4.2.1. Transcriptomics; 4.2.2. Proteomics; 4.2.3. Metabolomics
4.2.4. Epigenomics4.2.5. Population genomics; 4.3. Comparing the annotation to those of other genomes; 4.3.1. Comparative genomics; 4.3.2. Phylogenomics; 4.3.3. Ecogenomics; 5. Genomics of Plant-Microbe Interactions: What ́s Next?; 5.1. Systems biology; 5.2. Metagenomics; 5.3. The 1000 Fungal Genomes Project; 6. Conclusion; Acknowledgements; References; Chapter Two: Exploring the Transcriptome of Mycorrhizal Interactions; 1. Introduction; 2. Microarrays Versus Deep Sequencing; 3. Dual Transcriptomics of Plant-Fungus Interaction: Monitoring Both Partners at the Same Time
4. Combination of Transcriptomics and Microdissection5. Bioinformatic Tools for RNA-Seq Data Analysis; 5.1. Reads mapping onto reference sequences; 5.2. Transcriptome reconstruction; 5.3. Gene expression quantification; 6. Mycorrhizal Transcriptomes in the Genome Era; 6.1. Transcriptome of L. bicolor, a basidiomycete ectomycorrhizal fungus; 6.2. Transcriptome of T. melanosporum, an ascomycete ectomycorrhizal fungus; 6.3. Transcriptome of AM fungi; 6.4. Transcriptome of Paxillus involutus; 7. Outlook; Acknowledgements; Glossary; References
Chapter Three: Evolutionary and Adaptive Role of Transposable Elements in Fungal Genomes1. Introduction; 1.1. Fungal genomes; 1.1.1. Fungal genomics; 1.1.2. Fungal effectors; 1.2. TEs: General facts; 1.2.1. Classification; 1.2.2. Retrotransposons; 1.2.3. DNA transposons; 1.2.4. TEs in eukaryote genomes; 1.2.5. The main representative TE classes in genomes; 1.2.6. Selfish DNA?; 1.3. TEs: How genomes control proliferation; 1.3.1. How can genomes control TE proliferation?; 1.3.2. In fungi; 1.4. TEs in fungal genomes; 1.4.1. Main families found in fungal genomes
1.4.2. Repertoire of TEs and dating the invasion of fungal genomes
Description based upon print version of record.
Includes bibliographical references at the end of each chapters and indexes.
Description based on online resource; title from PDF title page (ebrary, viewed June 3, 2014).
Martin, Francis M., editor.
Bakkeren, Guus, contributor.
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