Do you need a genome or can a transcriptome alone be used to identify biosynthetic pathways? Why sequence and assemble a genome?

Question

[kristina.mahan]

Why get a genome assembled? Why not just do transcriptomics to identify biosynthetic pathways? Can someone tell me a reason to assemble a genome?

[kristina.mahan]

If I am only trying to identify a biosynthetic pathway of a chemical produced only in the root- will the genome help with that or can I only do transcriptomics? Pros and Cons?

[seidel]

trying to identify a biosynthetic pathway

I guess this depends on your criteria for identification. If you assemble a transcriptome from root, and then identify all the products via homology to known proteins, and your criteria is "I'll know it if I see these gene products" then this might be able to tell you if you see those gene products in your transcriptome. Pros: fast and easy - identify, catalog, score for presence/absence of known enzymes offering chemistry of interest. Cons: some of the enzymes might not be expressed at levels high enough for you to detect in your transcriptome, and you won't be able to tell if the genome can encode those things without sequencing the genome. Sequencing the genome would at least offer you the ability to do gene prediction, and then scan it for homology to members of your biosynthetic pathway of interest. The downside is that genome assembly and prediction takes another level of effort over transcriptome assembly.

Answer 1

[seidel]

Short answer: because there's more to the biology of an organism than biosynthetic pathways as represented in RNA Seq data. The genome contains regulatory information about all those pathways and their associated transcripts that you will not be able to study with the transcripts alone. How are you going to study chromatin dynamics with just a transcriptome? Not to mention, a transcriptome is typically always only partially defined, because you've never examined the coding potential of the genome under all possible conditions.

Answer 2

[Mensur Dlakic]

An even shorter answer: a transcriptome tells you only about genes that are active under a particular set of conditions, and in many cases that will be less than half of all genes. You would never know about the overall potential of an organism for biosynthesis (or indeed, for anything) by studying its transcriptome.