Hi, friends, I have an important question to discuss.
I want to study using phylogenomics approaches a genus with 20 species. Now thinking about phylogenetic reconstruction, what type of data was best for the study (DNA / RNA)? Four of the twenty species already have RNASEQ ready (by our group), my idea was to obtain the libraries of the other species and study the phylogenetics of the group?
This would be my postdoc project here in Brazil we have 2 years to complete, I have a good base with Transcriptomes.
You don't provide much information, so it is difficult to provide suggestions. For example, you don't say if the genus you want to study have small (and simple) or large (and complex) genomes. If the genomes are small and not very complex, I would consider more practical for this task using the gene set predicted from genome assemblies. In case the genomes are larger and more complex, using the transcriptomes is probably more feasible.
Start by performing a preliminary analysis with the four transcriptomes you already have at hand, try to find a couple more from the literature to complement this preliminary set. Proceed with the analysis you have planned - in general terms, transcriptome assembly, orthologous determination, pruning of the orthologous set and phylogeny reconstruction - and evaluate each step to check for potential problems and the quality of the results.
Thanks, so we only have two genomes assembled for the group I study. They are complex genomes and still undergoing improvements in annotations.