We have a non-model organism with no annotated genome, but with an annotated close relative. We would like to create an annotated transcriptome of this organism, while a complete genome is not really necessary at this point.
There is a not complete genomic sequence of this organism, done
We're not whether to go directly with a de-novo RNA-Seq workflow (e.g. Trinity), or the more traditional way via a de-novo DNA-Sequencing, try than with Velvet, SOAP, or any other tool to create a reference genome.
I suggest the first option of de novo transcriptome assembly (after RNA-seq). Note that for good assembly you need to calculate the depth of the RNA-seq required. If you are conducting an experiment with different samples for RNA-seq, do the RNA-seq to higher depth and this data @@can be used for de novo assembly and also for experimental analysis. This gives better results, in terms of coverage.
I work with a non-model insect which has a closely related annotated genome available. Based on what I did for my projects, I would suggest to do:
1. You should get a comprehensive representation of transcriptome by sampling different stages and tissues with high-coverage paired-end sequencing.
2. Then, you should use that data to do de novo transcriptome assembly using Trinity. You can do stage and tissue specific assemblies and you can do pulled reads assemblies too.
3. After that, you can annotate the transcriptome using BLAST2GO, Trinotate or reciprocal BLAST against the annotated transcriptome of the closely related species.
4. You can run one genomic sample alongside transcriptome (paired-end) in relatively moderate coverage which can help you to do a very draft genome assembly as it could help you many ways, as you can build some candidate contigs using BLAST or you can align it to closely reference genome to have a good understanding about difference of the genome content between two species. Those will help you to design an informed choice of genomic sampling for an extensive DNA-Seq/genome assembly project if you need to do in future.
De novo RNA-Seq will serve your purpose in a better way. It is a favored choice in case of unannotated or orphan genomes.
If your interest is to to create an annotated transcriptome only then De novo transcriptome assembly would be sufficient. But if you are interested in variation studies it is advisable to do both
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