Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry

Abstract Background Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. Findings Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar “Draper,” which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. Conclusions These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.

6. gene expression was analyzed across 14 different samples and total gene expression values were used to compare total gene expression across haplotypes. However, replicates were only available for fruit samples but not for all other samples. Hence, the findings here should be described as hints. Moreover, it should be explained how the fruit samples were treated in this analysis (was only one replicate used or the average count of all three?). 7. The citations of extended table 4 and 5 in the text seem to be wrong! I believe 5 is meant to be 4 and 6 (which doesn't exist) should be 5. This needs to be fixed. In general there seems to be a problem with the formatting ("error for extended table 2") and content of the extended tables. I would suggest to deposit them under a public data DOI instead of having them attached to the main manuscript. 8. I recommend that the manuscript is proof read in order to improve language, sentence structure, grammar and typing errors. Minor: 1. I would recommend not to use the term "expressed chromosomes". 2. in order to improve understanding the authors definition of the term 'haplotype' should be included in the manuscript since various definitions have been used in other publications. 3. The labels of the heatmaps in figure 3 are not readable. It would be nice to be able link the gene expression to the pathway. 4. The y-axis labels of figure S6-b are not readable 5. Figure S3 has a very low resolution

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