High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii)

Authors: YU, JIALI - University Of Tennessee; Hulse-Kemp, Amanda; Babiker, Ebrahiem; STATON, MARGARET - University Of Tennessee

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/13/2021
Publication Date: 11/1/2021
Citation: Yu, J., Hulse-Kemp, A.M., Babiker, E.M., Staton, M. 2021. High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). Horticulture Research. 8:228. https://doi.org/10.1038/s41438-021-00641-9.
DOI: https://doi.org/10.1038/s41438-021-00641-9

Interpretive Summary: Three native species of blueberries, V. darrowii Camp, V. myrsinites Lam., and V. virgatum were extensively used in southern highbush blueberry cultivars development. The evergreen blueberry V. darrowii is characterized by small leathery and thick leaves, short-statured and twiggy growth, good adaptation to the soil and climate of the southeast, resistance to leaf rust pathogen, and small firm berries with excellent flavor. There is a continual need to broaden the genetic base of SHB cultivars and enrich them with alleles from V. darrowii to enhance fruit quality and improve the level of tolerance to biotic and abiotic stresses. Despite the growing interest to utilize diverse V. darrowii accessions, progress has been limited due to lack of genomic resources. We present a chromosomal-level genome of V. darrowii generated by the combination of high throughput sequencing technologies. Results from this study detected attractive candidate genes and provided a good platform for further functional characterization of genes associated with heat tolerance and anthocyanin accumulation in blueberry.

Technical Abstract: Vaccinium darrowii Camp (2n=2x=24) is a native North American blueberry species and an important source of traits such as low chill requirement in commercial southern highbush blueberry breeding (V. corymbosum, 2n=4x=48). We present a chromosomal-level genome of V. darrowii generated by the combination of PacBio sequencing and high throughput chromatin conformation capture (Hi-C) scaffolding technologies, yielding a total length of 1.06 Gigabases (Gb). Over 97.8% of the genome sequences are scaffolded into 24 chromosomes representing the two haplotypes. The primary haplotype assembly of V. darrowii contains 34,809 protein-coding genes. Comparison to a V. corymbosum haplotype assembly reveals high collinearity between the two genomes with small intrachromosomal rearrangements in eight chromosome pairs. With small RNA sequencing, annotation was further expanded to include more than 200,000 small RNA loci and 638 microRNAs expressed in berry tissues. Transcriptome analysis across fruit development stages indicates that genes involved in photosynthesis are downregulated, while genes involved in flavonoid and anthocyanin biosynthesis are significantly increased at the late stage of berry ripening. A high-quality reference genome and accompanying annotation of V. darrowii is a significant new resource for assessing the evergreen blueberry contribution to the breeding of southern highbush blueberries.