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Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche

ABSTRACT: We sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis

ORGANISM(S): Ramichloridium luteum

PROVIDER: GSE100245 | GEO | 2017/10/04

SECONDARY ACCESSION(S): PRJNA391155

REPOSITORIES: GEO

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Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche.

Project description:BackgroundEctophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis.ResultsThe R. luteum genome was 28.18 Mb and encoded 9466 genes containing 1.85% repetitive elements. Compared with cell-penetrating pathogens, genes encoding plant cell wall degrading enzymes (PCWDEs), PTH11-like G protein-coupled receptors (GPCRs) and effectors were drastically reduced. In contrast, genes encoding cutinases and secretory lipases were strikingly expanded, and four of nine secretory lipases were probably acquired by horizontal gene transfer from Basidiomycota. Transcriptomic analysis revealed elevated expression of genes involved in cuticle degradation (cutinase, secretory lipase) and stress responses (melanin biosynthesis, aquaporins, lysozymes and HOG pathway).ConclusionsTaken together, our results highlight genomic features associated with evolution of surface niche adaptation by the ectophytic fungus R. luteum, namely the contraction of PCWDEs, PTH11-like GPCRs and effectors, and the expansion of cuticle degradation and stress tolerance.

| S-EPMC5602860 | biostudies-literature

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Proteomics analysis during fruit development of apple

Project description:Here, we conducted an tandem mass tag (TMT)-based proteomics analysis of apple fruit development over five growth stages. Our objective was to gain a global overview of the dynamics of apple fruit development and identify key regulatory networks and proteins that contribute to fruit development and the metabolism and accumulation of sugars and acids for fruit quality improvement.

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Microbacterium luteum strain:A18JL200

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Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes

Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes.

2010-11-05 | GSE24523 | GEO

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