It's been a few years, but the plant geneticists I used to work with until 2012 seemed to have to solve a lot of problems to get reliable full-genome sequences

It's been a few years, but the plant geneticists I used to work with until 2012 seemed to have to solve a lot of problems to get reliable full-genome sequences of de novo species (these have no reference assemblies to go by). Including what I had until then assumed was the simple act of just sampling DNA material: multiple consistent sites on the plants were sampled and this context was important not just for gene expression, but overall sanity checking of final assemblies (speaking of sanity checks: flow cytometry as well). Then there was setting up Illumina and 454 sequencing experiments, which seemed to involve quite a few iterations/experimentation in developing primers, choosing bead configuration, amplification procedures and a whole lot of other stuff I don't understand... And still, after all that, the literature did have a bunch of species that had already had a few genes sequenced using earlier methods and traditional PCRs, so the whole sample set was given this treatment as well, again as a sanity check and to get a strong reference to earlier results (1000+ of species, thousands of individual plants, each with multiple samples as I mentioned). And still, after all that... the evolutionary history of this group of plants still looks slightly different depending on which genes you looked at. And so now I know what a consensus tree is... and how much fun it is to see researchers have their software doing MCMC tree building run in just a few days on HPC compute clusters when they'd previously waited months :-)