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Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR
Published on: June 11, 2016
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Transcriptome characterisation and simple sequence repeat marker discovery in the seagrass Posidonia oceanica
D D'Esposito1, L Orrù2, E Dattolo1
1Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
Scientific Data
|December 21, 2016
Summary
Researchers created a comprehensive RNA-Seq dataset for Mediterranean seagrass (Posidonia oceanica), identifying gene predictions and Simple Sequence Repeats (SSR) markers to aid population genetics and functional variation studies.
Area of Science:
- Marine Biology
- Genomics
- Ecology
Background:
- Posidonia oceanica is a vital endemic Mediterranean seagrass, crucial for ecosystem services and biodiversity.
- Seagrass meadows inhabit depths from the surface to 40 meters, experiencing varying environmental conditions.
Purpose of the Study:
- To generate a comprehensive RNA-Seq dataset for Posidonia oceanica.
- To explore transcriptional diversity related to depth and light variations.
- To identify gene predictions and Simple Sequence Repeats (SSR) markers for future research.
Main Methods:
- RNA-Sequencing (RNA-Seq) was performed on P. oceanica specimens.
- Samples were collected at two different depths and two times of day.
- Bioinformatic analyses were used for assembly, annotation, and marker identification.
Main Results:
- A total of 79,235 contigs were assembled from 70,453,120 reads.
- 43,711 contigs were annotated, and 17,436 SSR markers were identified in 13,912 contigs.
Conclusions:
- The generated dataset provides a valuable resource for Posidonia oceanica research.
- New avenues are opened for analyzing population genetic features and functional variation.
- This study enhances our understanding of seagrass transcriptional responses to environmental factors.
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