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Article|01 Nov 2021|OPEN
High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii)
Jiali Yu1, Amanda M. Hulse-Kemp2,3, Margaret Staton 1,5, & Ebrahiem Babiker 4
1Genome Science and Technology Program, University of Tennessee, Knoxville, TN 37996, USA
2USDA-ARS Genomics and Bioinformatics Research Unit, Raleigh, NC, USA
3Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
4USDA-ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, USA
5Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA

Horticulture Research 8,
Article number: 228 (2021)
doi: 10.1038/hortres.2021.228
Views: 18

Received: 17 Apr 2021
Revised: 22 Jun 2021
Accepted: 13 Jul 2021
Published online: 01 Nov 2021

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 (Vaccinium corymbosum, 2n = 4x = 48). We present a chromosomal-scale 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, the 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.