Dataset Information

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici.

ABSTRACT: BACKGROUND: Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production. RESULTS: We assembled a 54.9Mb P. lycopersici draft genome sequence based on Illumina short reads, and annotated approximately 17,000 genes. The P. lycopersici genome is closely related to hemibiotrophs and necrotrophs, in agreement with the phenotypic characteristics of the fungus and its lifestyle. Several gene families related to host-pathogen interactions are strongly represented, including those responsible for nutrient absorption, the detoxification of fungicides and plant cell wall degradation, the latter confirming that much of the genome is devoted to the pathogenic activity of the fungus. We did not find a MAT gene, which is consistent with the classification of P. lycopersici as an imperfect fungus, but we observed a significant expansion of the gene families associated with heterokaryon incompatibility (HI). CONCLUSIONS: The P. lycopersici draft genome sequence provided insight into the molecular and genetic basis of the fungal lifestyle, characterizing previously unknown pathogenic behaviors and defining strategies that allow this asexual fungus to increase genetic diversity and to acquire new pathogenic traits.

SUBMITTER: Aragona M

PROVIDER: S-EPMC4234444 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici.

Aragona Maria M Minio Andrea A Ferrarini Alberto A Valente Maria Teresa MT Bagnaresi Paolo P Orrù Luigi L Tononi Paola P Zamperin Gianpiero G Infantino Alessandro A Valè Giampiero G Cattivelli Luigi L Delledonne Massimo M

BMC genomics 20140427

<h4>Background</h4>Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production.<h4>Results</h4>We assembled a 54.9Mb P. lycopersici draft genome sequence based on Illumina short reads, and ...[more]

PMID: 24767544

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Project description: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.

Project description:Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense, a wild relative of cultivated tomato (Solanum lycopersicum L.), is known to have exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the mechanism to salinity stress tolerance by S. chilense can be accomplished by comprehensive gene expression studies. In this study 1-month-old seedlings of S. chilense and S. lycopersicum were subjected to salinity stress through application of sodium chloride (NaCl) solution. Through RNA-sequencing here we have studied the differences in the gene expression patterns. A total of 386 million clean reads were obtained through RNAseq analysis using the Illumina HiSeq 2000 platform. Clean reads were further assembled de novo into a transcriptome dataset comprising of 514,747 unigenes with N50 length of 578 bp and were further aligned to the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 265,158 genes that were differentially expressed in response to salt treatment, 134,566 and 130,592 genes were significantly up and down-regulated, respectively. Upon placing all the differentially expressed genes (DEG) in known signaling pathways, it was evident that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca2+ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and up-regulation of multiple genes involved in various biological processes in chilense under salinity were identified. Through pathway analysis of DEGs, "Wnt signaling pathway" was identified as a novel pathway for the response to the salinity stress. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transporters, osmotic regulation, defense and stress response, homeostasis and transcription factors were not only salt-induced but also showed higher expression in S. chilense as compared to S. lycopersicum. Thus indicating that these genes may have an important role in salinity tolerance in S. chilense. Overall, the results of this study improve our understanding on possible molecular mechanisms underlying salt tolerance in plants in general and tomato in particular.

Dataset Information

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici.

Publications

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici.

Similar Datasets

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