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  4. Phragmites australis Transcriptome Assembly Optimization

Phragmites australis Transcriptome Assembly Optimization

Dates

Start Date
2012-08
End Date
2021-05
Publication Date

Citation

Tao, F., Fan, C., Liu, Y., Sivakumar, S., Kowalski, K.P., and Golenberg, E.M., 2023, Phragmites australis Transcriptome Assembly Optimization: U.S. Geological Survey data release, https://doi.org/10.5066/P9NRU97T.

Summary

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 [...]

Contacts

Point of Contact :
Kurt P Kowalski
Process Contact :
Edward M. Golenberg, Feng Tao
Originator :
Feng Tao, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P Kowalski, Edward M. Golenberg
Metadata Contact :
Taaja R. Tucker-Silva
Publisher :
U.S. Geological Survey
Distributor :
U.S. Geological Survey - ScienceBase
SDC Data Owner :
Great Lakes Science Center
USGS Mission Area :
Ecosystems

Attached Files

Click on title to download individual files attached to this item.

Phragmites_australis_Transcriptome_Assembly_Optimization-20230323.xml
Original FGDC Metadata
View 		182.7 KB application/fgdc+xml
Data_S1.csv 6.6 MB text/csv
Data_S2.csv 612.01 KB text/csv
Data_S3.csv 1.01 MB text/csv
Data_S4.csv 224.45 KB text/csv
Data_S5.csv 18.53 MB text/csv
Data_S6.csv 37.8 KB text/csv
Data_S7.csv 1.52 MB text/csv
Data_S8.csv 57.74 KB text/csv
Phragmites_anno.csv 170.82 MB text/csv
cdhit.zip 93.9 MB application/zip
GapClosed.zip 116.11 MB application/zip
no_cdhit.zip 132.3 MB application/zip
shannon.zip 154.54 MB application/zip
transabyss.zip 90.54 MB application/zip
Trinity.zip 55.33 MB application/zip
Trinity-GG.zip 6.16 MB application/zip
cdhit.fa.transdecoder.pep.zip 40.25 MB application/zip
TMM.EXPR.matrix.zip 2.87 MB application/zip

Purpose

The purpose was to construct a Phragmites australis transcriptome with biologically accurate and complete transcripts which would facilitate the functional annotation of transcripts and downstream analyses on the nonnative P. australis subspecies. Many transcriptome assembly studies use only one plant tissue type or a single assembly tool (e.g., Trinity), but the transcriptomes in this release were assembled from RNA from multiple plant tissues and from the generation of multiple transcriptomes by different assembly tools and parameter settings and by collating them as one non-redundant transcriptome, which may produce more robust and reliable results.

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Communities

  • Great Lakes Science Center (GLSC)
  • USGS Data Release Products

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Additional Information

Identifiers

Type Scheme Key
DOI https://www.sciencebase.gov/vocab/category/item/identifier doi:10.5066/P9NRU97T

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