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Open AccessArticle

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.

1
Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
2
Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
3
Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
4
Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
5
International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
6
Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
7
Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
*
Authors to whom correspondence should be addressed.
We dedicate this paper to the memory of our colleague Dirk K. Hincha who passed away during the preparation of this manuscript.
Int. J. Mol. Sci. 2020, 21(21), 8148; https://doi.org/10.3390/ijms21218148
Received: 28 September 2020 / Revised: 20 October 2020 / Accepted: 30 October 2020 / Published: 31 October 2020
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
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 aus 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. View Full-Text
Keywords: dehydrins; natural genetic variation; PacBio Sequel; RNA-Seq; SMRT sequencing; de novo reference transcriptomes; rice dehydrins; natural genetic variation; PacBio Sequel; RNA-Seq; SMRT sequencing; de novo reference transcriptomes; rice
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MDPI and ACS Style

Schaarschmidt, S.; Fischer, A.; Lawas, L.M.F.; Alam, R.; Septiningsih, E.M.; Bailey-Serres, J.; Jagadish, S.V.K.; Huettel, B.; Hincha, D.K.; Zuther, E. Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. Int. J. Mol. Sci. 2020, 21, 8148.

AMA Style

Schaarschmidt S, Fischer A, Lawas LMF, Alam R, Septiningsih EM, Bailey-Serres J, Jagadish SVK, Huettel B, Hincha DK, Zuther E. Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. International Journal of Molecular Sciences. 2020; 21(21):8148.

Chicago/Turabian Style

Schaarschmidt, Stephanie; Fischer, Axel; Lawas, Lovely M.F.; Alam, Rejbana; Septiningsih, Endang M.; Bailey-Serres, Julia; Jagadish, S. V.K.; Huettel, Bruno; Hincha, Dirk K.; Zuther, Ellen. 2020. "Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L." Int. J. Mol. Sci. 21, no. 21: 8148.

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