I am currently trying to find out what options are available for assembly of RNAseq reads of many individuals within a diverse panel of plants. I work in corn, in which we currently have a few reference genomes available. I currently have access to RNAseq data from seedling stage plants in a wide diversity panel and am trying to figure out what is the best assembly approach is most appropriately. I currently see three options:

1. Reference genome assembly using one of the references: This would unfortunately miss the diversity that would be captured in the panel.
2. De novo assembly using something like Trinity. This seems like a viable option however I would think that it would be more optimal to take advantage of the references we have available.
3. Genome-guided de novo assembly: I see that Trinity has the option to accept a reference genome to use as a guide during the de novo assembly process: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Genome-Guided-Trinity-Transcriptome-Assembly

Among these options, the guided de novo assembly seems the most promising. My questions are: 1) Is there other options besides Trinity for this sort of approach? 2) Do any of them accept multiple genomes for the assembly process?