The symbiotic hydra Hydra viridissima has a stable symbiotic relationship with the green alga Chlorella. This hydra appears to cospeciate with the symbiotic alga, and some strains are known to have strain-specific host/symbiont combinations. To investigate the mechanism of the specificity between host and symbiont, we explored the effect of the removal or exchange of symbionts in two distantly related H. viridissima strains (K10 and M9). In this study, we compared the gene expression of symbiont-removed, symbiont-exchanged hosts for each strain. The data include the raw read fastaq, assembled sequences, and read counts of RNA-seq.  We also attached the results of differential gene expression analyses for all combinations of the hosts. 

We used six experimental groups (K10ori, M9ori, K10apo, M9apo, K10exc, and M9exc) for the RNA-seq analysis. The analysis was performed with 150 bp paired-end reads on an Illumina HiSeq 4000 and Illumina MiSeq. 

The low-quality reads were filtered out with the following criteria.

1, Low-quality ends (QV < 30) and adapter sequences were trimmed using cutadapt. 

2, Short reads (<20 bp) were discarded for quality control using cutadapt. 

3, Any remaining rRNA sequences were filtered out using SortMeRNA 2. 

After quality filtering, de novo assembly was performed on the reads generated from HiSeq and MiSeq using Trinity, and the contigs less than 200 bp were discarded. Next, reads from HiSeq were mapped to the assembled contigs using salmon. Next, clustering of the assembled contigs and read counting were performed with Corset. Finally, a similarity search of the clustered contigs against UniProtKB was conducted using BLASTX with an e-value cut-off of 1e-5 to remove sequences from the symbiotic chlorellae and annotate the contigs. We calculated e-values against homologous protein sequences of Opisthokonta and Viridiplantae in UniProtKB and those of H. vulgaris in TrEMBL. Contigs whose e-values of the best hits against Opisthokonta and Hydra sequences were smaller than those against Viridiplantae were considered hydra contigs. These hydra contigs were annotated with UniProtKB Swiss-Prot. The remaining unannotated contigs were annotated with entries from H. vulgaris, whose whole genome was sequenced and annotated UniProtKB TrEMBL to find hydra-specific genes. 

To find orthologues between K10 and M9, protein sequences translated from the contigs were estimated using TransDecoder (https://github.com/TransDecoder/TransDecoder), and an orthogroup, which is the set of genes that are descended from a single gene in the last common ancestor, was inferred by Orthofinder using those protein sequences and sequences from H. vulgaris in the RefSeq database.