Yes, you can use a reference genome from a related species to assemble transcripts of a target species. This approach is known as de novo transcriptome assembly. However, it is important to keep in mind that using a reference genome from a different species as a basis for assembly may not result in a highly accurate representation of the target species transcriptome, as the two species may have different gene structures, gene expression patterns, and splicing patterns.

Additionally, the quality of the assembly will depend on the similarity between the target species and reference species genomes. Therefore, it is often recommended to use a reference genome from a closely related species, or to use a combination of multiple reference genomes to improve the accuracy of the assembly.