Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing
Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing w...
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| Format: | Article |
| Language: | English |
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Wiley
2017-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2017/9184731 |
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| author | Gang Nie Linkai Huang Xiao Ma Zhongjie Ji Yajie Zhang Lu Tang Xinquan Zhang |
| author_facet | Gang Nie Linkai Huang Xiao Ma Zhongjie Ji Yajie Zhang Lu Tang Xinquan Zhang |
| author_sort | Gang Nie |
| collection | DOAJ |
| description | Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis. |
| format | Article |
| id | doaj-art-2249c0d9eaf64cb09d17302e8a05ab20 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-2249c0d9eaf64cb09d17302e8a05ab202025-02-03T01:30:47ZengWileyInternational Journal of Genomics2314-436X2314-43782017-01-01201710.1155/2017/91847319184731Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA SequencingGang Nie0Linkai Huang1Xiao Ma2Zhongjie Ji3Yajie Zhang4Lu Tang5Xinquan Zhang6Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, ChinaDepartment of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, ChinaDepartment of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN 47906, USADepartment of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, ChinaDepartment of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, ChinaDepartment of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, ChinaMiscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.http://dx.doi.org/10.1155/2017/9184731 |
| spellingShingle | Gang Nie Linkai Huang Xiao Ma Zhongjie Ji Yajie Zhang Lu Tang Xinquan Zhang Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing International Journal of Genomics |
| title | Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing |
| title_full | Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing |
| title_fullStr | Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing |
| title_full_unstemmed | Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing |
| title_short | Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing |
| title_sort | enriching genomic resources and transcriptional profile analysis of miscanthus sinensis under drought stress based on rna sequencing |
| url | http://dx.doi.org/10.1155/2017/9184731 |
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