De novo transcriptome assembly of Sorghum bicolor variety Taejin
Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variet...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2016-06-01
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| Series: | Genomics Data |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596016300617 |
| _version_ | 1818298473537077248 |
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| author | Yeonhwa Jo Sen Lian Jin Kyong Cho Hoseong Choi Sang-Min Kim Sun-Lim Kim Bong Choon Lee Won Kyong Cho |
| author_facet | Yeonhwa Jo Sen Lian Jin Kyong Cho Hoseong Choi Sang-Min Kim Sun-Lim Kim Bong Choon Lee Won Kyong Cho |
| author_sort | Yeonhwa Jo |
| collection | DOAJ |
| description | Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers. |
| first_indexed | 2024-12-13T04:35:53Z |
| format | Article |
| id | doaj.art-ae7e2bf43e75487190ac15ef6dc2e722 |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-12-13T04:35:53Z |
| publishDate | 2016-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-ae7e2bf43e75487190ac15ef6dc2e7222022-12-21T23:59:26ZengElsevierGenomics Data2213-59602016-06-018C11711810.1016/j.gdata.2016.05.002De novo transcriptome assembly of Sorghum bicolor variety TaejinYeonhwa Jo0Sen Lian1Jin Kyong Cho2Hoseong Choi3Sang-Min Kim4Sun-Lim Kim5Bong Choon Lee6Won Kyong Cho7Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of KoreaCollege of Crop Protection and Agronomy, Qingdao Agricultural University, Qingdao, Shandong 266109, ChinaThe Taejin Genome Institute, Gadam-gil 61, Hoengseong, 25239, Republic of KoreaDepartment of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of KoreaCrop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, Republic of KoreaCrop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, Republic of KoreaCrop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, Republic of KoreaDepartment of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of KoreaSorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.http://www.sciencedirect.com/science/article/pii/S2213596016300617RNA-SeqSorghum bicolorTranscriptomeVariety |
| spellingShingle | Yeonhwa Jo Sen Lian Jin Kyong Cho Hoseong Choi Sang-Min Kim Sun-Lim Kim Bong Choon Lee Won Kyong Cho De novo transcriptome assembly of Sorghum bicolor variety Taejin Genomics Data RNA-Seq Sorghum bicolor Transcriptome Variety |
| title | De novo transcriptome assembly of Sorghum bicolor variety Taejin |
| title_full | De novo transcriptome assembly of Sorghum bicolor variety Taejin |
| title_fullStr | De novo transcriptome assembly of Sorghum bicolor variety Taejin |
| title_full_unstemmed | De novo transcriptome assembly of Sorghum bicolor variety Taejin |
| title_short | De novo transcriptome assembly of Sorghum bicolor variety Taejin |
| title_sort | de novo transcriptome assembly of sorghum bicolor variety taejin |
| topic | RNA-Seq Sorghum bicolor Transcriptome Variety |
| url | http://www.sciencedirect.com/science/article/pii/S2213596016300617 |
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