Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

Background Vaccinium is an economically important genus of berry crops in the family Ericaceae. Given the numerous hybridizations and polyploidization events among Vaccinium species, the taxonomy of this genus has remained uncertain and the subject of long debate. Therefore, the availability of more genomic resources for Vaccinium can provide useful tools for phylogenetic resolution, species identification, authentication of berry food products, and a framework for genetic engineering. Results In this study, we assembled five Vaccinium chloroplast sequences representing the following 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 ). Two complete plastid genomes were achieved using long-read PacBio sequencing, while three draft sequences were obtained using short-read Illumina sequencing. Comparative analyses also included other previously available Vaccinium chloroplast sequences, especially the commercially important species V. macrocarpon (cranberry). The Vaccinium chloroplast genomes exhibited a circular quadripartite structure, with an overall highly conserved synteny and sequence identity among them. Despite their high similarity, we identified some polymorphic regions in terms of expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, and single nucleotide polymorphisms. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events during northern and southern highbush blueberry domestication. Conclusions Our results enrich the genomic data availability for new Vaccinium species by sequencing and assembling the chloroplast DNA of major economically important berry types. Additional whole plastome analyses including more samples and wild species will be useful to obtain a refined knowledge of the maternal breeding history of blueberries and increase phylogenetic resolution at low taxonomic levels. ### Competing Interest Statement The authors have declared no competing interest. * SHB : Southern Highbush Blueberry NHB : Northern Highbush Blueberry RB : Rabbiteye Blueberry LB : Lowbush Blueberry BB : Bilberry CB : Cranberry cpDNA : chloroplast DNA SSR : Simple Sequence Repeat SNP : Single Nucleotide Polymorphism ITS : Internal Transcribed Spacer IRs : Inverted repeats LSC : Large Single Copy SSC : Small Single Copy rRNA : ribosomal RNA tRNA : transfer RNAs