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

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.

Molecular characterization of SPL gene family during flower morphogenesis and regulation in blueberry

“…This was also supported by the number of homologous pairs identified in the comparative genomes of blueberry with Arabidopsis and rice, and it was hypothesized that divergence of the common ancestor of rice and dicotyledonous plants occurred before the divergence of blueberry and Arabidopsis. In blueberry, a total of two pairs of tandem duplications were identified and 11 pairs of segmental duplication, presumably segmental duplication playing a very important role in VcSPL gene amplification, in agreement with previously [ 43 , 53 ]. It is clear that blueberry and bilberry show a high degree of clustering at the end of the evolutionary branch of SPLs , and 36 homologous pairs were identified, indicating a high degree of convergence in their relationship, consistent with the previous study [ 43 ].…”

“…In blueberry, a total of two pairs of tandem duplications were identified and 11 pairs of segmental duplication, presumably segmental duplication playing a very important role in VcSPL gene amplification, in agreement with previously [ 43 , 53 ]. It is clear that blueberry and bilberry show a high degree of clustering at the end of the evolutionary branch of SPLs , and 36 homologous pairs were identified, indicating a high degree of convergence in their relationship, consistent with the previous study [ 43 ].…”

“…To investigate the evolutionary relationships of blueberries, we performed the identification of bilberry SPL family members based on recently published diploid blueberry(bilberry) data [ 43 ], identifying a total of 24, with gene names and positional information in Supplementary Table 2 , and then constructed phylogenetic trees for the amino acid sequences of Arabidopsis, tobacco, rice, and bilberry. The 56 SPL structural domains were divided into six subclasses based on topological relationships (Fig.…”

“…To classify the evolutionary relationships of the VcSPLs gene family, the SPL protein sequences of Arabidopsis thaliana [ 39 ], rice ( Oryza sativa ) [ 41 ], tobacco ( Nicotiana tabacum L. ) [ 42 ], grape ( Vitis vinifera ) [ 11 ] and diploid blueberry ( Vaccinium darrowii ) [ 43 ] were aligned using the CluastW algorithm and MEGA11 software [ 44 ], where diploid bilberry SPL family members were identified in the same way to tetraploid blueberry, with gene names and location information in the Supplementary Table 2 . Phylogenetic analysis based on amino acid sequence alignment was performed using the neighbor-joining (NJ) method with Bootstrap tests on 1000 resamples, and for more reliable phylogenetic analysis, maximum likelihood (ML) was also considered [ 45 ].…”

Full-length fruit transcriptomes of southern highbush (Vaccinium sp.) and rabbiteye (V. virgatum Ait.) blueberry

“…The GO annotation for this genome was around 57%, which was a significant improvement from the previous draft genome. More recently, a reference genome for Vaccinium darrowii, an evergreen wild blueberry has been generated [8,9]. However, there is still no available genome for southern highbush or rabbiteye blueberries, those usually grown in the southeastern parts of the US.…”