Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarpon Ait.) and a wild relative

Authors: DIAZ-GARCIA, LUIS - University Of Wisconsin; RODRIGUEZ-BONILLA, LORRAINE - University Of Wisconsin; ROHDE, JESSICA - University Of Wisconsin; SMITH, TYLER - Agriculture And Agri-Food Canada; Zalapa, Juan

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2019
Publication Date: 4/10/2019
Citation: Diaz-Garcia, L., Rodriguez-Bonilla, L., Rohde, J., Smith, T., Zalapa, J.E. 2019. Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarpon Ait.) and a wild relative. Genes. 10(4):291. https://doi.org/10.3390/genes10040291.
DOI: https://doi.org/10.3390/genes10040291

Interpretive Summary: Breeding efforts in the American or large cranberry, a North American perennial fruit crop of great importance, have been hampered by the limited genetic variability observed among commercial cultivars. Most of the cultivars used by cranberry growers today were derived from a few wild accessions bred in the 1950s. A closely related wild species, the small cranberry, may be useful to improve traits in the American cranberry. Although both of these species have previously been utilized in genetic studies, genomic and comparative studies are still lacking. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two minor differences. Additional sequencing revealed high genetic variation in both species using multiple individuals. This research is important because it revealed that the cranberry species are more genetic similar than previously known, even despite marked trait differences. Thus, based on the results of this study, cranberry wild germplasm could be an important genetic resource to incorporate novel traits and increase diversity in breeding programs. The results of this research will be useful to breeders when using small cranberry to improve fruit quality traits such as fruit size and chemical content and acclimation such as cold hardiness and heat stress.

Technical Abstract: Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry and could be useful to improve fruit quality such as phytochemical content, and given their northern distribution (V. microcarpum has been collected at 70° N in North America and Europe), could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V. microcarpum. Finally, we provided important data regarding the polyploid origin of V. oxycoccos.