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Velasco VME, Ferreira A, Zaman S, Noordermeer D, Ensminger I, Wegrzyn JL. A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir). G3 (BETHESDA, MD.) 2023; 13:jkac304. [PMID: 36454025 PMCID: PMC10468028 DOI: 10.1093/g3journal/jkac304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 10/19/2022] [Indexed: 12/02/2022]
Abstract
Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.
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Affiliation(s)
| | - Alyssa Ferreira
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Sumaira Zaman
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Devin Noordermeer
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Jill L Wegrzyn
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
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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. Int J Mol Sci 2020; 21:ijms21218148. [PMID: 33142722 PMCID: PMC7663775 DOI: 10.3390/ijms21218148] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/05/2023] Open
Abstract
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.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
| | - Dirk K. Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
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