Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops

Vaccinium is a large genus of shrubs that includes a handful of
economically important berry crops. Given the numerous hybridizations and
polyploidization events, the taxonomy of this genus has remained the
subject of long debate. In addition, berries and berry-based products are
liable to adulteration, either fraudulent or unintentional due to
misidentification of species. The availability of more genomic information
could help achieve higher phylogenetic resolution for the genus, provide
molecular markers for berry crop identification, and a framework for
efficient genetic engineering of chloroplasts. Therefore, in this study,
we assembled five Vaccinium chloroplast sequences representing the
economically relevant berry types: northern highbush blueberry (V.
corymbosum), southern highbush blueberry (V. corymbosum hybrids),
rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium),
and bilberry (V. myrtillus). Comparative analyses showed that the
Vaccinium chloroplast genomes exhibited an overall highly conserved
synteny and sequence identity among them. Polymorphic regions included the
expansion/contraction of inverted repeats, gene copy number variation,
simple sequence repeats, indels, and single nucleotide polymorphisms.
Based on their in silico discrimination power, we suggested variants that
could be developed into molecular markers for berry crop identification.
Phylogenetic analysis revealed multiple origins of highbush blueberry
plastomes, likely due to the hybridization events that occurred during
northern and southern highbush blueberry domestication.