Chromosome-level genome assembly of the American cranberry (Vaccinium macrocarpon Ait.) and its wild relative Vaccinium microcarpum

Authors: DIAZ-GARCIA, LUIS - INSTITUTO NACIONAL DE INVESTIGACIONES FORESTALES Y AGROPECUARIAS (INIFAP); GARCIA-ORTEGA, LUIS FERNANDO - GUANAJUATO CAMPUS OF CINVESTAV; GONZÁLEZ RODRÍGUEZ, MARIA - GUANAJUATO CAMPUS OF CINVESTAV; DELAYE, LUIS - GUANAJUATO CAMPUS OF CINVESTAV; IORIZZO, MASSIMO - NORTH CAROLINA STATE UNIVERSITY; Zalapa, Juan

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2021
Publication Date: 2/10/2021
Citation: Diaz-Garcia, L., Garcia-Ortega, L., González-Rodríguez, M., Delaye, L., Iorizzo, M., Zalapa, J.E. 2021. Chromosome-level genome assembly of the American cranberry (Vaccinium macrocarpon Ait.) and its wild relative Vaccinium microcarpum. Frontiers in Plant Science. 12. Article 633310. https://doi.org/10.3389/fpls.2021.633310.
DOI: https://doi.org/10.3389/fpls.2021.633310

Interpretive Summary: The American cranberry is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genetic code database. These new high quality cranberry genetic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level. Here, we report the first chromosome-scale genetic code assembly of cranberry, cultivar Stevens, and a draft genetic code of its closest wild relative species. We assembled more than 92% of the estimated cranberry genetic code into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative analysis, divergence, and evolution with other plant species, including close relatives such as blueberry and kiwifruit. Finally, we identified a cluster of genetic sequences related to color variation in fruit. Our analysis of these genes indicate that they act as pigment biosynthesis regulators in cranberry. The chromosome-level cranberry genetic code, and the draft genetic code of its closest wild relative species, provide a much-needed resource for further investigation of the genetic architecture underlying trait variation. These genetic codes will support cranberry improvement efforts by facilitating the discovery of novel trait-gene associations useful in molecular based breeding strategies.

Technical Abstract: The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors in close proximity with a large QTL for anthocyanin variation in fruit. Phylogenetics suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.