Plant phylogenomics : approaches to make phylogenic inference more reliable Correct phylogenetic inference is especially hard on very shallow and deep taxonomic levels. On intraspecific intrageneric levels widely used genetic fingerprinting techniques (AFLP SSR) tend to yield volatile results partially because bands of equal size on the gel should not necessarily be orthologous and absence of a band does not necessarily mean absence of a character as it might be caused by experimental setup (see Kumar et al. 2009). At the same time at this taxonomic range commonly used phylogenetic markers such as nuclear ITS regions and chloroplast spacers genes are only of limited help due to lack of informative characters to resolve tree structure end even medium size data sets suffer from lack of resolution. This work demonstrates the benefit of introducing cpDNA based phylogenomic methodology to shallow level taxonomic research. Well resolved tree structure allowed for the first time to reveal phylogenetic affinities of the maternal line of domesticated apple sorts. Three distinct chloroplast DNA lineages present in apple cultivars diverged before the origin of agriculture. ...