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Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation

Citation

Koenig, Kristen (2022), Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation, Dryad, Dataset, https://doi.org/10.5061/dryad.8cz8w9grb

Abstract

Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays, we characterize eye formation in Doryteuthis pealeii Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris, and the eye placode is the sole source of retinal tissue. Functional assays demonstrate that Notch signaling is required for photoreceptor cell differentiation and retinal organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of both conserved and convergent mechanisms.

Methods

Squid were acquired at the Marine Biological Laboratory, Woods Hole, MA. Embryos were cultured at 20°C. Two embryos from the same egg sac of each stage, from 16-27, were prepared in TRIzol, phase separated and transferred to a Qiagen RNeasy column. Libraries were prepared after Meyer et al. (2009, 2012). Libraries were combined at equal volume and sequenced using 454 technology at the University of Texas, Austin. The 454 raw reads were processed using custom Perl scripts (https://github.com/Eli-Meyer/sequence_processing). Trimmed reads were assembled using Newbler v.2.6. Annotation was performed using BLASTX and custom Perl scripts mapped against the UniProt database. Illumina data were processed for quality using custom Perl scripts (https://github.com/Eli-Meyer/sequence_processing). All raw reads and annotated data have been deposited at the NCBI (SRA accession numbers SRP065414 and SRP066528).