Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.)
<p>Blueberry is an economically important berry crop. Both production and consumption of blueberries have increased sharply worldwide in recent years at least partly due to their known health benefits. The development of improved genomic resources for blueberry, such as a well-assembled genome and transcriptome, could accelerate breeding through genomic-assisted approaches. To enrich available transcriptome data and identify genes potentially involved in fruit quality, RNA sequencing was performed on fruit tissue from two northern-adapted hybrid blueberry breeding populations. RNA-seq was carried out using the Illumina HiSeqTM 2500 platform. Because of the absence of a reference-grade genome for blueberry, a transcriptome was de novo assembled from this RNA-seq data and other publicly available transcriptome data from blueberry downloaded from the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) using Trinity. After removing redundancy, this resulted in a dataset of 91,861 blueberry unigenes. This unigene dataset was functionally annotated using the NCBI-Nr protein database. All raw reads from the breeding populations were deposited in the NCBI SRA with accession numbers SRR6281886, SRR6281887, SRR6281888, and SRR6281889. The de novo transcriptome assembly was deposited at NCBI Transcriptome Shotgun Assembly (TSA) database with accession number GGAB00000000. These data will provide real expression evidence for the blueberry genome gene prediction and gene functional annotation and a reference transcriptome for future gene expression studies involving blueberry fruit. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.).</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1016/j.dib.2019.104390">https://doi.org/10.1016/j.dib.2019.104390</a> </p></li></ul><p></p>
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2019
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Subjects: | Crop and pasture production, Genomics and transcriptomics, Genetics, Plant biology not elsewhere classified, NP301, northern-adapted hybrid, data.gov, ARS, |
Online Access: | https://figshare.com/articles/dataset/Data_from_Dataset_of_de_novo_assembly_and_functional_annotation_of_the_transcriptome_of_blueberry_Vaccinium_spp_/24853257 |
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dat-usda-us-article248532572019-08-12T00:00:00Z Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) Xinpeng Qi (17481360) Elizabeth L. Ogden (11001270) Mark K. Ehlenfeldt (17481363) Lisa J. Rowland (17477190) Crop and pasture production Genomics and transcriptomics Genetics Plant biology not elsewhere classified NP301 northern-adapted hybrid data.gov ARS <p>Blueberry is an economically important berry crop. Both production and consumption of blueberries have increased sharply worldwide in recent years at least partly due to their known health benefits. The development of improved genomic resources for blueberry, such as a well-assembled genome and transcriptome, could accelerate breeding through genomic-assisted approaches. To enrich available transcriptome data and identify genes potentially involved in fruit quality, RNA sequencing was performed on fruit tissue from two northern-adapted hybrid blueberry breeding populations. RNA-seq was carried out using the Illumina HiSeqTM 2500 platform. Because of the absence of a reference-grade genome for blueberry, a transcriptome was de novo assembled from this RNA-seq data and other publicly available transcriptome data from blueberry downloaded from the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) using Trinity. After removing redundancy, this resulted in a dataset of 91,861 blueberry unigenes. This unigene dataset was functionally annotated using the NCBI-Nr protein database. All raw reads from the breeding populations were deposited in the NCBI SRA with accession numbers SRR6281886, SRR6281887, SRR6281888, and SRR6281889. The de novo transcriptome assembly was deposited at NCBI Transcriptome Shotgun Assembly (TSA) database with accession number GGAB00000000. These data will provide real expression evidence for the blueberry genome gene prediction and gene functional annotation and a reference transcriptome for future gene expression studies involving blueberry fruit. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.).</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1016/j.dib.2019.104390">https://doi.org/10.1016/j.dib.2019.104390</a> </p></li></ul><p></p> 2019-08-12T00:00:00Z Dataset Dataset 10.1016/j.dib.2019.104390 https://figshare.com/articles/dataset/Data_from_Dataset_of_de_novo_assembly_and_functional_annotation_of_the_transcriptome_of_blueberry_Vaccinium_spp_/24853257 CC BY 4.0 |
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National Agricultural Library of USDA |
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Crop and pasture production Genomics and transcriptomics Genetics Plant biology not elsewhere classified NP301 northern-adapted hybrid data.gov ARS |
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Crop and pasture production Genomics and transcriptomics Genetics Plant biology not elsewhere classified NP301 northern-adapted hybrid data.gov ARS Xinpeng Qi (17481360) Elizabeth L. Ogden (11001270) Mark K. Ehlenfeldt (17481363) Lisa J. Rowland (17477190) Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) |
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<p>Blueberry is an economically important berry crop. Both production and consumption of blueberries have increased sharply worldwide in recent years at least partly due to their known health benefits. The development of improved genomic resources for blueberry, such as a well-assembled genome and transcriptome, could accelerate breeding through genomic-assisted approaches. To enrich available transcriptome data and identify genes potentially involved in fruit quality, RNA sequencing was performed on fruit tissue from two northern-adapted hybrid blueberry breeding populations. RNA-seq was carried out using the Illumina HiSeqTM 2500 platform. Because of the absence of a reference-grade genome for blueberry, a transcriptome was de novo assembled from this RNA-seq data and other publicly available transcriptome data from blueberry downloaded from the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) using Trinity. After removing redundancy, this resulted in a dataset of 91,861 blueberry unigenes. This unigene dataset was functionally annotated using the NCBI-Nr protein database. All raw reads from the breeding populations were deposited in the NCBI SRA with accession numbers SRR6281886, SRR6281887, SRR6281888, and SRR6281889. The de novo transcriptome assembly was deposited at NCBI Transcriptome Shotgun Assembly (TSA) database with accession number GGAB00000000. These data will provide real expression evidence for the blueberry genome gene prediction and gene functional annotation and a reference transcriptome for future gene expression studies involving blueberry fruit. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.).</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1016/j.dib.2019.104390">https://doi.org/10.1016/j.dib.2019.104390</a> </p></li></ul><p></p> |
format |
Dataset |
author |
Xinpeng Qi (17481360) Elizabeth L. Ogden (11001270) Mark K. Ehlenfeldt (17481363) Lisa J. Rowland (17477190) |
author_facet |
Xinpeng Qi (17481360) Elizabeth L. Ogden (11001270) Mark K. Ehlenfeldt (17481363) Lisa J. Rowland (17477190) |
author_sort |
Xinpeng Qi (17481360) |
title |
Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) |
title_short |
Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) |
title_full |
Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) |
title_fullStr |
Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) |
title_full_unstemmed |
Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.) |
title_sort |
data from: dataset of de novo assembly and functional annotation of the transcriptome of blueberry (vaccinium spp.) |
publishDate |
2019 |
url |
https://figshare.com/articles/dataset/Data_from_Dataset_of_de_novo_assembly_and_functional_annotation_of_the_transcriptome_of_blueberry_Vaccinium_spp_/24853257 |
work_keys_str_mv |
AT xinpengqi17481360 datafromdatasetofdenovoassemblyandfunctionalannotationofthetranscriptomeofblueberryvacciniumspp AT elizabethlogden11001270 datafromdatasetofdenovoassemblyandfunctionalannotationofthetranscriptomeofblueberryvacciniumspp AT markkehlenfeldt17481363 datafromdatasetofdenovoassemblyandfunctionalannotationofthetranscriptomeofblueberryvacciniumspp AT lisajrowland17477190 datafromdatasetofdenovoassemblyandfunctionalannotationofthetranscriptomeofblueberryvacciniumspp |
_version_ |
1802722144043401216 |