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HIGH RESOLUTION ANNOTATION OF ZEBRAFISH TRANSCRIPTOME USING LONG-READ SEQUENCING

German Nudelman, Antonio Frasca, Brandon Kent, Kirsten Edepli-Sadler, Stuart C. Sealfon, Martin J. Walsh, Elena Zaslavsky
doi: https://doi.org/10.1101/174821
German Nudelman
1Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
2Center for Advanced Research on Diagnostic Assays (CARDA)
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Antonio Frasca
3Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Brandon Kent
4Department of Development and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Kirsten Edepli-Sadler
5Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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Stuart C. Sealfon
1Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
2Center for Advanced Research on Diagnostic Assays (CARDA)
3Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Martin J. Walsh
3Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
6Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Elena Zaslavsky
1Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
2Center for Advanced Research on Diagnostic Assays (CARDA)
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ABSTRACT

With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 high confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and non-coding RNAs, isoform switching occurrences and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8 kb transcript spanning multiple miR-430 elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted August 10, 2017.
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HIGH RESOLUTION ANNOTATION OF ZEBRAFISH TRANSCRIPTOME USING LONG-READ SEQUENCING
German Nudelman, Antonio Frasca, Brandon Kent, Kirsten Edepli-Sadler, Stuart C. Sealfon, Martin J. Walsh, Elena Zaslavsky
bioRxiv 174821; doi: https://doi.org/10.1101/174821
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HIGH RESOLUTION ANNOTATION OF ZEBRAFISH TRANSCRIPTOME USING LONG-READ SEQUENCING
German Nudelman, Antonio Frasca, Brandon Kent, Kirsten Edepli-Sadler, Stuart C. Sealfon, Martin J. Walsh, Elena Zaslavsky
bioRxiv 174821; doi: https://doi.org/10.1101/174821

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