Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L.
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted soluti...
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| Format: | Article |
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/21/8148 |
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| author | Stephanie Schaarschmidt Axel Fischer Lovely Mae F. Lawas Rejbana Alam Endang M. Septiningsih Julia Bailey-Serres S. V. Krishna Jagadish Bruno Huettel Dirk K. Hincha Ellen Zuther |
| author_facet | Stephanie Schaarschmidt Axel Fischer Lovely Mae F. Lawas Rejbana Alam Endang M. Septiningsih Julia Bailey-Serres S. V. Krishna Jagadish Bruno Huettel Dirk K. Hincha Ellen Zuther |
| author_sort | Stephanie Schaarschmidt |
| collection | DOAJ |
| description | The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant <i>aus</i> cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes. |
| first_indexed | 2024-03-10T15:11:06Z |
| format | Article |
| id | doaj.art-93271ae868d0408c819b6602a6669f52 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:11:06Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-93271ae868d0408c819b6602a6669f522023-11-20T19:19:51ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012121814810.3390/ijms21218148Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L.Stephanie Schaarschmidt0Axel Fischer1Lovely Mae F. Lawas2Rejbana Alam3Endang M. Septiningsih4Julia Bailey-Serres5S. V. Krishna Jagadish6Bruno Huettel7Dirk K. Hincha8Ellen Zuther9Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, GermanyMax Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, GermanyMax Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, GermanyCenter for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USADepartment of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USACenter for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USAInternational Rice Research Institute, DAPO Box 7777, Metro Manila 1301, PhilippinesMax Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, GermanyMax Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, GermanyMax Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, GermanyThe wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant <i>aus</i> cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.https://www.mdpi.com/1422-0067/21/21/8148dehydrinsnatural genetic variationPacBio SequelRNA-SeqSMRT sequencingde novo reference transcriptomes |
| spellingShingle | Stephanie Schaarschmidt Axel Fischer Lovely Mae F. Lawas Rejbana Alam Endang M. Septiningsih Julia Bailey-Serres S. V. Krishna Jagadish Bruno Huettel Dirk K. Hincha Ellen Zuther Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L. International Journal of Molecular Sciences dehydrins natural genetic variation PacBio Sequel RNA-Seq SMRT sequencing de novo reference transcriptomes |
| title | Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L. |
| title_full | Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L. |
| title_fullStr | Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L. |
| title_full_unstemmed | Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L. |
| title_short | Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in <i>Oryza sativa</i> L. |
| title_sort | utilizing pacbio iso seq for novel transcript and gene discovery of abiotic stress responses in i oryza sativa i l |
| topic | dehydrins natural genetic variation PacBio Sequel RNA-Seq SMRT sequencing de novo reference transcriptomes |
| url | https://www.mdpi.com/1422-0067/21/21/8148 |
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