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Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii)

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arillastrum gummiferum Tristaniopsis glauca Syzygium longifolium

PROVIDER: GSE106750 | GEO | 2018/11/08

REPOSITORIES: GEO

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Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii).

Project description:The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where Myrtaceae are the dominant or codominant species, as well as in several commercial nurseries. It is now considered as a significant threat to ecosystems biodiversity and Myrtaceae-related economy. The use of predictive molecular markers for resistance against myrtle rust is currently the most cost-effective and ecological approach to control the disease. Such an approach for neo Caledonian endemic Myrtaceae species was not possible because of the lack of genomic resources. The recent advancement in new generation sequencing technologies accompanied with relevant bioinformatics tools now provide new research opportunity for work in non-model organism at the transcriptomic level. The present study focuses on transcriptome analysis on three Myrtaceae species endemic to New Caledonia (Arillastrum gummiferum, Syzygium longifolium and Tristaniopsis glauca) that display contrasting responses to the pathogen (non-infected vs infected). Differential gene expression (DGE) and variant calling analysis were conducted on each species. We combined a dual approach by using 1) the annotated reference genome of a related Myrtaceae species (Eucalyptus grandis) and 2) a de novo transcriptomes of each species.

| S-EPMC6362868 | biostudies-literature

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [SYZLO-EUCGR]

Project description:Finding predictive molecular markers for resistance against Myrtle rust may help to identify resistant plants and provide a means of maintaining Myrtaceae production in nursery, especially for ecosystems restoration purposes. Sequence polymorphism involving in differentiate expressed genes are particularly relevant for disease resistance marker design. We sequenced the transcriptomes of resistant and susceptible individuals of three endemic host species: Arillastrum gummiferum, Tristaniopsis glauca and Syzygium longifolium. The rust phenotype of the individuals of each species was defined as "infected" (considered as susceptible) and "healthy" (considered as resistant). We described here a pre-breeding methodology to find disease resistance markers by combining next-generation sequencing, differential gene expression (DGE) and SNP calling. DGE was conducted in parallel using the only one available sequenced Myrtaceae genome (Eucalyptus grandis) and a de novo assembly transcriptome from each species. The edgeR tests if a gene is DE between “infected” individuals versus “healthy” ones. If the fold change log (FC = infected/healthy) is greater than 0, the gene is thus overexpressed in the infected individuals (considered as susceptible).

2018-11-08 | GSE106749 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [SYZLO-DENOVO]

2018-11-08 | GSE106747 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-EUCGR]

2018-11-08 | GSE106736 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-DENOVO]

2018-11-08 | GSE106735 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-FAR-EUCGR]

2018-11-08 | GSE106746 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-FAR-DENOVO]

2018-11-08 | GSE106741 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-EUCGR]

2018-11-08 | GSE106740 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-DENOVO]

2018-11-08 | GSE106738 | GEO

Impact of Austropuccinia psidii (myrtle rust) on Myrtaceae-rich wet sclerophyll forests in south east Queensland.

Project description:In April 2010, Austropuccinia psidii (formerly Puccinia psidii) was detected for the first time in Australia on the central coast of New South Wales. The fungus spread rapidly along the east coast and can now be found infecting vegetation in a range of native forest ecosystems with disease impacts ranging from minor leaf spots to severe shoot and stem blight and tree dieback. Localised extinction of some plant species has been recorded. In 2014, the impact of A. psidii was observed for the first time in a wet sclerophyll site with a rainforest understory, dominated by species of Myrtaceae, in Tallebudgera Valley, south east Queensland, Australia. This study aimed to determine the impact of A. psidii on individual species and species composition. Here we provide quantitative and qualitative evidence on the significant impact A. psidii has in native ecosystems, on a broader range of species than previously reported. Archirhodomyrtus beckleri, Decaspermum humile, Gossia hillii and Rhodamnia maideniana are in serious decline, with significant increases in tree mortality over the period of our study. This research further highlights the potential of this invasive pathogen to negatively impact native ecosystems and biodiversity.

| S-EPMC5697815 | biostudies-literature

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