Suggestion for de novo transcriptome assembly of a plant with high heterozygosity

Question

[seta]

Hi all,

I've got Illumina sequencing reads (100 bp, PE) from a non-model dioecious plant (two genotypes, one is sensitive to treatment and another is tolerant) with high heterozygosity. What's your suggestion for de novo transcriptome assembly and RNA-seq analysis given the high heterozygosity of sample? Is it better to pool all reads or using separate reads from two genotypes for de novo assembly? Thanks for your comments