The developmental transcriptome of Parhyale hawaiensis

Abstract

For decades, most of our understanding of fundamental biological processes has originated from the study of model organisms. However, despite their simplicity and amenability for laboratory research these models in many cases are not representative of their groups. As such, new organisms that are more representative of animals in their phylum have emerged as vital tools. For instance, among the arthropods, the most numerous and speciose phyla of metazoans, the crustacean Parhyale hawaiensis has been established as a model alongside several existing insect models. Parhyale’s winning points are its phylogenetic position (sister group of insects) and, unlike Drosophila melanogaster, an embryonic development pathway that resembles most of the animals in its phylum. However, to date no developmental transcriptome of Parhyale exists and its small RNA complement has not been examined. Furthermore, the techniques we use for visually assessing crustacean embryonic development are rudimentary, in an era where biology is becoming increasingly quantitative. In this study, we have established protocols to collect and stage embryos spanning the entire embryonic development of Parhyale. We defined seven different embryonic time- points, to assess key developmental events including maternal-to-zygotic transition, germband extension and morphogenesis, and performed RNA-Seq and small RNA- Seq. From these datasets, we have provided the first comprehensive annotation of mRNAs, microRNAs and piRNAs in this species. Due to the temporal resolution of our data, we have been able to follow the dynamic expression of these transcripts throughout embryogenesis and have been able, for the first time in a crustacean, to predict the targets of all microRNAs and analyse their relationship with the mRNAs they regulate. Finally, we have developed new imaging protocols to allow the detection and quantification of mRNAs at single molecule and single cell resolution, in Parhyale and in embryonic and adult tissues from other arthropod species. Our transcriptome datasets will facilitate the study of gene regulatory processes throughout crustacean development. Our imaging protocols will facilitate the study of a wide range of topics such as segmentation, cell-to-cell transcriptional variation, as well as any specific cell fate behaviours that rely in transcriptional variation. The results presented here will help to cement Parhyale as an attractive model organism for evolutionary developmental biology studies.

Date of Award	1 Aug 2021
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Sam Griffiths-Jones (Supervisor) & Matthew Ronshaugen (Supervisor)