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Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq

Anthony Bayega, Spyros Oikonomopoulos, Eleftherios Zorbas, Yu Chang Wang, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Kostas D Mathiopoulos, Jiannis Ragoussis
doi: https://doi.org/10.1101/478172
Anthony Bayega
1McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
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Spyros Oikonomopoulos
1McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
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Eleftherios Zorbas
2Laboratory of Genomics and Molecular Biology, Department of Biochemistry & Biotechnology, University of Thessaly, Thessaly, Greece
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Yu Chang Wang
1McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
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Maria-Eleni Gregoriou
2Laboratory of Genomics and Molecular Biology, Department of Biochemistry & Biotechnology, University of Thessaly, Thessaly, Greece
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Konstantina T Tsoumani
2Laboratory of Genomics and Molecular Biology, Department of Biochemistry & Biotechnology, University of Thessaly, Thessaly, Greece
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Kostas D Mathiopoulos
2Laboratory of Genomics and Molecular Biology, Department of Biochemistry & Biotechnology, University of Thessaly, Thessaly, Greece
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Jiannis Ragoussis
1McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
3Department of Bioengineering, McGill University, Montréal, Québec, Canada
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Abstract

The olive fruit fly or olive fly (Bactrocera oleae) is the most important pest of cultivated olive trees. Like all insects the olive fly undergoes complete metamorphosis. However, the transcription dynamics that occur during early embryonic development have not been explored, while detailed transcriptomic analysis in the absence of a fully annotated genome is challenging. We collected olive fly embryos at hourly intervals for the first 6 hours of development and performed full-length cDNA-Seq using a purpose designed SMARTer cDNA synthesis protocol followed by sequencing on the MinION (Oxford Nanopore Technologies). We generated 31 million total reads across the timepoints (median yield 4.2 million per timepoint). The reads showed 98 % alignment rate to the olive fly genome and 91 % alignment rate to the NBCI predicted B. oleae gene models. Over 50 % of the expressed genes had at least one read covering its entire length validating our full-length RNA-Seq procedure. Expression of 68 % of the predicted B. oleae genes was detected in the first six hours of development. We generated a de novo transcriptome assembly of the olive fly and identified 3553 novel genes and a total of 79,810 transcripts; a fourfold increase in transcriptome diversity compared to the NCBI predicted transcriptome. On a global scale, the first six hours of embryo development were characterized by dramatic transcriptome changes with the total number of transcripts per embryo dropping to half from the first hour to the second hour of embryo development. Clustering of genes based on temporal co-expression followed by gene-set enrichment analysiss of genes expressed in the first six hours of embryo development showed that genes involved in transcription and translation, macro-molecule biosynthesis, and neurodevelopment were highly enriched. These data provide the first insight into the transcriptome landscape of the developing olive fly embryo. The data also reveal transcript signatures of sex development. Overall, full-length sequencing of the cDNA molecules permitted a detailed characterization of the isoform complexity and the transcriptional dynamics of the first embryonic stages of the B. oleae.

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Posted November 24, 2018.
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Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq
Anthony Bayega, Spyros Oikonomopoulos, Eleftherios Zorbas, Yu Chang Wang, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Kostas D Mathiopoulos, Jiannis Ragoussis
bioRxiv 478172; doi: https://doi.org/10.1101/478172
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Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq
Anthony Bayega, Spyros Oikonomopoulos, Eleftherios Zorbas, Yu Chang Wang, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Kostas D Mathiopoulos, Jiannis Ragoussis
bioRxiv 478172; doi: https://doi.org/10.1101/478172

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