I'd like to create an annotated genome for a small eukaryotic organism. Ultimately, it will be used to conduct a transcriptomic analysis using illumina paired-end RNA-seq data that I obtained previously. There are no sequenced genes for the species, but there are sequenced genomes/genes for other members of the genus (it's a very small genus). The reason we've decided to annotate the genome is that this species is the most distantly related.
Would I still able to blast genes from other species within the genus? Or would a genome annotation be possible at all? I know that de novo assembly is an option, but I was hoping for a genome annotation over de novo if possible
Any advice is welcome regarding where to begin/which softwares/packages etc.