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The genome assembly of the fungal pathogen Pyrenochaeta lycopersici from Single-Molecule Real-Time sequencing sheds new light on its biological complexity
- Source :
- PLoS ONE, Vol 13, Iss 7, p e0200217 (2018), PLoS ONE
- Publication Year :
- 2018
- Publisher :
- Public Library of Science (PLoS), 2018.
-
Abstract
- The first draft genome sequencing of the non-model fungal pathogen Pyrenochaeta lycopersici showed an expansion of gene families associated with heterokaryon incompatibility and lacking of mating-type genes, providing insights into the genetic basis of this "imperfect" fungus which lost the ability to produce the sexual stage. However, due to the Illumina short-read technology, the draft genome was too fragmented to allow a comprehensive characterization of the genome, especially of the repetitive sequence fraction. In this work, the sequencing of another P. lycopersici isolate using long-read Single Molecule Real-Time sequencing technology was performed with the aim of obtaining a gapless genome. Indeed, a gapless genome assembly of 62.7 Mb was obtained, with a fraction of repetitive sequences representing 30% of the total bases. The gene content of the two P. lycopersici isolates was very similar, and the large difference in genome size (about 8 Mb) might be attributable to the high fraction of repetitive sequences detected for the new sequenced isolate. The role of repetitive elements, including transposable elements, in modulating virulence effectors is well established in fungal plant pathogens. Moreover, transposable elements are of fundamental importance in creating and re-modelling genes, especially in imperfect fungi. Their abundance in P. lycopersici, together with the large expansion of heterokaryon incompatibility genes in both sequenced isolates, suggest the presence of possible mechanisms alternative to gene re-assorting mediated by sexual recombination. A quite large fraction (~9%) of repetitive elements in P. lycopersici, has no homology with known classes, strengthening this hypothesis. The availability of a gapless genome of P. lycopersici allowed the in-depth analysis of its genome content, by annotating functional genes and TEs. This goal will be an important resource for shedding light on the evolution of the reproductive and pathogenic behaviour of this soilborne pathogen and the onset of a possible speciation within this species.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Sequence assembly
lcsh:Medicine
Plant Science
Pathology and Laboratory Medicine
01 natural sciences
Genome
Pyrenochaeta lycopersici
Database and Informatics Methods
Medicine and Health Sciences
DNA, Fungal
lcsh:Science
Phylogeny
Genetics
Fungal Pathogens
Multidisciplinary
Fungal genetics
Plant Fungal Pathogens
Eukaryota
Chromosome Mapping
Genomics
Fungal
Medical Microbiology
Pathogens
Genome, Fungal
Sequence Analysis
Research Article
Bioinformatics
Plant Pathogens
Mycology
Biology
Research and Analysis Methods
Microbiology
DNA sequencing
03 medical and health sciences
Ascomycota
Computer Systems
Fungal Genetics
Genome size
Gene
Microbial Pathogens
Fungal Genomics
Sequence Assembly Tools
lcsh:R
Organisms
Fungi
Biology and Life Sciences
Computational Biology
Molecular Sequence Annotation
DNA
Sequence Analysis, DNA
Comparative Genomics
Plant Pathology
biology.organism_classification
Genome Analysis
DNA Transposable Elements
030104 developmental biology
lcsh:Q
Sequence Alignment
010606 plant biology & botany
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 13
- Issue :
- 7
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....af821fc36ab9b1df1c38b2e2aa6e0944