M. occulta and M. oculata are tunicate speices found on the Northwestern coast of France, in Roscoff. They look very similar in their adult stages, however have alternate body plans in their larval stage. M. oculata goes through typical tunicate development, with a tadpole larvae. M. occulta, on the hand forgoes developing a tail and goes into metamorphosis shortly after hatching. These species are able to be cross fertilized producing a hybir with half a tail. Using RNA-seq, we sequenced and examined three developmental time points for M. occulta, M. oculata and their hybird.
Genomes from Aniseed were scaffolded using redundans with reads from the original assemblies, and M. oculata being used as reference for M. occulta because M. oculata assembly is less fragmented and closely related.
Transcriptomes were assembled using Trinity genome guided command this was done to improve the gene models that are also found on Aniseed. Next, transcripts were converting into supertranscripts to give a gene view to aid in cross speices comparisons. Transcripts were then filtered for short (less than 100 amino acids) fragments using TransDecoder. Finally, transcripts scaffolded with TransPS](https://bioinformatics.cs.vt.edu/zhanglab/software/transps/) using C. robusta protein sequences as a reference. Genome and transcriptome assemblies can be found on open science framework
M. occulta and M. oculata reads were mapped to their respective transcriptomes using bowtie2 and eXpress streaming pipeline. The Molgula hybrids were mapped onto both parent transcriptomes in the same manner in order to quantify allele specific expression.
EdgeR was used to idenify differentially expressed genes.