Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s,respectively,and in part owing to their f lavors and health-promoting benefits are now cultivated and consumed worldwide.The industry continues to face a wide variety of production challenges(e.g.disease pressures),as well as a demand for higher-yielding cultivars with improved fruit quality characteristics.Unfortunately,molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops.Here,we describe the construction and analysis of the first pangenome for both blueberry and cranberry.Our analysis of these pangenomes revealed both crops exhibit great genetic diversity,including the presence-absence variation of 48.4%genes in highbush blueberry and 47.0%genes in cranberry.Auxiliary genes,those not shared by all cultivars,are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites,including compounds previously associated with improving fruit quality traits.The discovery of thousands of genes,not present in the previous reference genomes for blueberry and cranberry,will serve as the basis of future research and as potential targets for future breeding efforts.The pangenome,as a multiple-sequence alignment,as well as individual annotated genomes,are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database.Lastly,the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Defining the‘HoneySweet’insertion event utilizing NextGen sequencing and a de novo genome assembly of plum(Prunus domestica)

HoneySweet’plum(Prunus domestica)is resistant to Plum pox potyvirus,through an RNAi-triggered mechanism.Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum.DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event.To confirm the transgene arrangement of the insertion event,‘HoneySweet’DNA was subjected to whole genome sequencing using Illumina short-read technology.Results indicated two different insertion events,one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side,flanked by plum DNA.To determine the locations of the two transgene insertions,a phased plum genome assembly was developed from the commercial plum‘Improved French’.A subset of the scaffolds(2447)that were>10 kb in length and representing,>95%of the genome were annotated and used for alignment against the‘HoneySweet’transgene reads.Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart,however we were unable to identify which scaffold(s)represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars.Regardless,there was no evidence of any gene(s)being interrupted as a result of the insertions.Furthermore,RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.