Even though organisms whose reference sequences are not available, gene expression data can be obtained by aligning RNA-seq reads to transctiptome de novo assemblies.
This page decribes how to submit such gene expression data.
Gene expression data
Submit gene or contig expression data (counts) as processed data files of GEA. Please include a table describing relationships between contigs and genes, or RefSeq/Ensembl IDs, in processed data files.
Transcriptome Shotgun Assembly
Please consider to submit assembled transcriptome sequences to DDBJ Transcriptome Shotgun Assembly (TSA). Gene annotation is not required for TSA. A set of assemblies from samples can be submitted as single set of TSA sequences.