Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest

Abstract The olive fruit fly, Bactrocera oleae , is the most important pest for but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development first time this organism. Sequencing on MinION platform generated over 31 million reads. Over 50% of expressed genes had at least one read covering its entire length validating our full-length approach. a de novo transcriptome assembly and identified 1768 new total 79,810 isoforms; fourfold increase diversity compared current NCBI predicted transcriptome. Absolute per allowed an insight into dramatic re-organization maternal transcripts. further Zelda as possible regulator zygotic genome activation B. provide insights maternal-to-zygotic transition. These data show utility improving non-model organisms lack fully annotated genome, potential targets sterile insect technic approaches, landscape developing fly embryo.