Genomic and transcriptomic resources for the tropical ascidian Phallusia philippinensis

Due to remarkably stereotyped development and small numbers of cells, ascidian embryos are invaluable as models for investigating the principles of chordate development at single-cell resolution. Established model species of ascidians, such as Ciona spp. and Phallusia mammillata, are primarily distributed in temperate waters, and natural populations become scarce in the summer due to rising water temperatures. However, Phallusia philippinensis is a tropical/subtropical species that is closely related to P. mammillata and shares the feature of highly transparent embryos, which facilitates live imaging and optical analyses. Its accessibility in warmwater habitats makes P. philippinensis a promising alternative model for imaging-based analyses, particularly in tropical regions or during the summer. We present comprehensive genomic transcriptomic resources that have been resolved according to the developmental stage for P. philippinensis. The assembled genome spans 150.2 Mb and comprises 407 contigs with an N50 of 909 kb and a GC content of 42.0%. Transcriptomes from 5 organs and 9 distinct embryonic stages were used to construct a gene model, which revealed 20,928 genes with a high BUSCO completeness score of 88.6%. Functional annotations were assigned to 16,507 genes using the UniProt and RefSeq databases. We integrated these resources into a new constructed genomic browser, which can be used easily by all researchers. These new resources are immediately applicable to comparative developmental studies of gene expression and regulation in ascidian embryos and will comprehensively cover the off-season of reproduction for model ascidians.