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

Abstract

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 crops 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 crops 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.

The First Complete Chloroplast Genome Sequence of Mortiño (Vaccinium floribundum) and Comparative Analyses with Other Vaccinium Species

“…The Vaccinieae, a tribe belonging to the Ericaceae family, is a unique and megadiverse group in its floral and vegetative morphology. Vaccinium is the only genus within this tribe that occurs in temperate and tropical zones, including the Northern Hemisphere, Southeast Asia, Malaysia, and the South American tropics (from Mexico to northern Argentina) [1][2][3][4]. This genus has more than 450-500 species [5], many of them identified as popular berry crops (e.g., blueberry, V. angustifolium; cranberry, V. macrocarpon Aiton; huckleberry, V. ovatum Pursh) [6,7].…”

“…It has a quadripartite structure with two inverted repeats (IRa and IRb, 20-28 kb in length) separated by two regions of unique DNA: large (LSC, 80-90 kb in length) and small (SSC, 16-27 kb in length) single copy regions [7,[26][27][28]. These regions are used as "super-barcodes" in phylogenic reconstructions and evolutionary history inference, as they provide sequence-based polymorphisms [4] and have unique genetic properties (i.e., uniparental inheritance, well-preserved gene arrangements, small size, haploidy, and non-recombinant nature) [4,7,26].…”

“…To date, 16 cp genome sequences from Vaccinium species have been published: V. macrocarpon (2), V. duclouxii, V. microcarpum, V. fragile, V. oldhamii, V. bracteatum, V. vitis-idaea, V. uliginosum, V. japonicum, V. corymbosum (3), V. virgatum, V. angustifolium, and V. myrtillus (Table S1) [4,6,7,27,[29][30][31][32][33][34]. Most of these are reported as plastome assemblies, without any information on comparative analyses [4].…”

“…To date, 16 cp genome sequences from Vaccinium species have been published: V. macrocarpon (2), V. duclouxii, V. microcarpum, V. fragile, V. oldhamii, V. bracteatum, V. vitis-idaea, V. uliginosum, V. japonicum, V. corymbosum (3), V. virgatum, V. angustifolium, and V. myrtillus (Table S1) [4,6,7,27,[29][30][31][32][33][34]. Most of these are reported as plastome assemblies, without any information on comparative analyses [4]. Yet, these types of studies are important, as they can reveal interesting structural variations, such as IR or gene loss, insertions/deletions (InDels), inversions, substitutions, genome rearrangements, and translocations associated with environmental adaptations [7,35].…”

Genomic and evolutionary relationships among wild and cultivated blueberry species

“…The primary goal was to introduce adaptation for lower chill requirements [31]. The phylogenetic analysis based on the nuclear genomewide SNP data indicated that SHB and NHB are more closely related to each other [21,32]. In PCA [33].…”