Nonnative Phragmites australis (common reed) is widely distributed across North America and insufficient knowledge of P. australis has impeded the efficiency of management. To aid in Phragmites management and future studies, we used RNA-seq data from multiple types of plant tissue to construct forty-nine P. australis transcriptomes via different assembly tools and multiple parameter settings, resulting in seven assembled transcriptomes for further comprehensive assessments. The optimal transcriptome (“cd-hit”) was selected for functional annotation and downstream analyses. This data release contains the seven assembled transcriptomes, and data derived from the optimal transcriptome (functional annotations, tissue-specific expression patterns, putative transcription factors, and simple sequence repeats markers).
Citation Information
| Publication Year | 2023 |
|---|---|
| Title | Phragmites australis Transcriptome Assembly Optimization |
| DOI | 10.5066/P9NRU97T |
| Authors | Feng Tao, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P Kowalski, Edward M. Golenberg |
| Product Type | Data Release |
| Record Source | USGS Digital Object Identifier Catalog |
| USGS Organization | Great Lakes Science Center |
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Optimization and application of non-native Phragmites australis transcriptome assemblies
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Optimization and application of non-native Phragmites australis transcriptome assemblies
Phragmites australis (common reed) has a cosmopolitan distribution and has been suggested as a model organism for the study of invasive plant species. In North America, the non-native subspecies (ssp. australis) is widely distributed across the contiguous 48 states in the United States and large parts of Canada. Even though millions of dollars are spent annually on Phragmites management, insufficiAuthorsFeng Tao, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P. Kowalski, Edward M Golenberg - Connect