Sequencing coverage for phylogenomic studies

Question

[tiagobellintani]

Hi friends?

As some of you know, the new NextSeq technology allows you to tailor coverage to your needs, I would like to know what would be an ideal coverage for phylogenomic studies based on transcriptomes

[GenoMax]

I am not sure what tailoring you are referring to here. NextSeq is a type of Illumina sequencer. It is going to produce a certain amount of data (a range of bp yield based on quality of libraries and specification limits of particular flowcell type). It would be your responsibility to pool appropriate amount of libraries together to spread that total yield out over the samples you have.

What kind of phylogenomic studies do you have in mind exactly? It was not very clear as to what you are proposing in this and your last (Phylogenomic study: suggestions and tips ) question. Are you planning to use entire transcriptomes to do this?

[h.mon]

As you said in another thread you have already four sequenced transcriptomes, and should use this data to evaluate the optimal depth of sequencing for your needs. You can down sample this data and evaluate the effect of sequencing depth in the completeness of orthologous gene matrix.

Additional steps to ensure good quality data for phylotranscriptomics would be to extract RNA from the same tissues / cell type / life stage from all samples, to maximize the chance the genes (and isoforms) being expressed are the same for all samples.

[tiagobellintani]

Thank you, good suggestion. My idea was to make the most of these assemblies that I have, primarily for the cost of sequencing (Brazil = high value per sequencing). I intend to select some regions of the assemblies that I have and start working with regions already known, that is, to assemble a more specific matrix, without the need to sequence the RNAtotal;