The evolution of DNA sequencing technologies (NextGen Sequencing) has deeply changed the way of designing sequencing projects for comparative genomics. For a cost and an acquisition time reduced by several orders of magnitude, a comparative genomics project nowadays consists in sequencing several complete genomes related to a reference genome. To cope with this inflow of data, it is necessary to have automatic methods performing good quality annotation. With the exploration of the large evolutionary range of hemiascomycete yeasts, the Génolevures Consortium earned a good expertise of genome annotation and of the methods used in comparative genomics.