De novo transcriptome assembly and annotations for wheat curl mite (Aceria tosichella)

Metadata Updated: November 19, 2019

To study the impact of wheat streak mosaic virus on global gene expression in wheat curl mite, we generated a de novo transcriptome assembly using 50 x 50 paired end reads from the Illumina HiSeq 2500. Reads were assembled using Trinity (version 2.0.6) and contigs greater than 200 nt were retained. All assembled transcripts were annotated using the Trinotate pipeline using blastp searches against the Swiss-prot/Uni-Prot database, blastx searches against the Swiss-prot/Uni-Prot databases, HMM searches against the Pfam-A database, blastp searches against the non-redundant protein database, and signalP and tmHMM predictions. To reduce noise from low abundance transcripts not well supported by the data, we filtered the assembly to retain only those transcripts with TPM values [HTML_REMOVED]=0.5.

Access & Use Information

Public: This dataset is intended for public access and use. License: Creative Commons CCZero

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Dates

Metadata Created Date October 12, 2018
Metadata Updated Date November 19, 2019

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date October 12, 2018
Metadata Updated Date November 19, 2019
Publisher USDA NAL
Unique Identifier a0383cef-ac36-486d-9980-9e72530e5977
Maintainer
Scully, Erin
Maintainer Email
Public Access Level public
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 4ca348df-a86c-4f44-a850-758be2caf8b5
Harvest Source Id 50ca39af-9ddb-466d-8cf3-84d67a204346
Harvest Source Title USDA JSON
License https://creativecommons.org/publicdomain/zero/1.0/
Data Last Modified 2019-08-05
Program Code 005:040
Source Datajson Identifier True
Source Hash 971628eb17d8a48d405b8318093eee9a5d85cc03
Source Schema Version 1.1

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