Category Archives: Allgemein

Mitogenomics is not dead… an example from glycerid annelids

Recently we published a paper using genome skimming to generate markers for phylogenetic analysis of glycerid annelids (Richter et al. 2015). We are interested in this group, as we are also working on the evolution of venom system of these annelids (e.g. von Reumont et al. 2014). Genome skimming basically means low coverage genome sequencing using NGS techniques. E.g., in the case of a coverage of 5x, it is expected that every part of the genome is (on average) sequenced 5 times. This is far from enough to assemble┬áthe nuclear genome. However, sequences which are present in higher copy number within the cell will have also a higher coverage than the average. E.g., we can easily expect 100 or more mitochondria per cell and consequently they will be also represented in a much higher coverage after sequencing. Using this method, complete mitochondria can be reconstructed quite easily from shallowly sequenced nuclear genomes. So we did this for 19 glycerid specimens and one outgroup (Goniadidae). After assembling the data, we were able to recover complete mitochondria for 14 species. For the other cases, several large contigs containing the mitochondrial genes could be found. Moreover, we also retrieved the ribosomal cluster (18S, ITS1, 5.8S, ITS2, 28S), which is also presented in many (tandemly repeated) copies per genome. Using the sequence data, we were able to reconstruct a fairly supported phylogeny of glycerids (Fig. 1), which will help us in the future to understand venom evolution in this group. Continue reading Mitogenomics is not dead… an example from glycerid annelids

Advertisements