Cerasus x kanzakura cv. 'Atami-zakura' Whole Genome v1.0 Assembly & Annotation
Kenta Shirasawa, Akihiro Itai, Sachiko Isobe, Genome sequencing and analysis of two early-flowering cherry (Cerasus × Kanzakura) varieties, 'Kawazu-zakura' and 'Atami-zakura', DNA Research, 2021;, dsab026, https://doi.org/10.1093/dnares/dsab026
To gain genetic insights into the early-flowering phenotype of ornamental cherry, also known as sakura, 20 we determined the genome sequences of two early-flowering cherry (Cerasus × kanzakura) varieties, 21 'Kawazu-zakura' and 'Atami-zakura'. Since the two varieties are interspecific hybrids, likely derived from 22 crosses between Cerasus campanulata (early-flowering species) and Cerasus speciosa, we employed the 23 haplotype-resolved sequence assembly strategy. Genome sequence reads obtained from each variety by 24 single molecule real-time sequencing (SMRT) were split into two subsets, based on the genome sequence 25 information of the two probable ancestors, and assembled to obtain haplotype-phased genome sequences. 26 The resultant genome assembly of 'Kawazu-zakura' spanned 519.8 Mb with 1,544 contigs and an N50 27 value of 1,220.5 kb, while that of 'Atami-zakura' totaled 509.6 Mb with 2,180 contigs and an N50 value of 28 709.1 kb. A total of 72,702 and 69,528 potential protein-coding genes were predicted in the genome 29 assemblies of 'Kawazu-zakura' and 'Atami-zakura', respectively. Gene clustering analysis identified 2,634 30 clusters uniquely presented in the C. campanulata haplotype sequences, which might contribute to its 31 early-flowering phenotype. Genome sequences determined in this study provide fundamental information 32 for elucidating the molecular and genetic mechanisms underlying the early-flowering phenotype of 33 ornamental cherry tree varieties and their relatives.
Homology of the Cerasus x kanzakura ATM Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2021-09) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
Functional annotation for the Cerasus x kanzakura ATM Genome v1.0 are available for download below. The Cerasus x kanzakura Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Cerasus x kanzakura genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.