Cerasus x kanzakura cv. 'Kawazu-zakura' Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NameCerasus x kanzakura cv. 'Kawazu-zakura' Whole Genome v1.0 Assembly & Annotation
MethodFalcon, Canu
SourcePACBIO SMRT Cerasus x kanzakura KWZ
Date performed2021-11-09

Publication

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

Abstract

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

Homology of the Cerasus x kanzakura Kawazu-zakura 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. 

 

Protein Homologs

Cerasus x kanzakura v1.0 proteins with NCBI nr homologs (EXCEL file) ckanzakura_KWZ_v1.0_vs_nr.xlsx.gz
Cerasus x kanzakura v1.0 proteins with NCBI nr (FASTA file) ckanzakura_KWZ_v1.0_vs_nr_hit.fasta.gz
Cerasus x kanzakura v1.0 proteins without NCBI nr (FASTA file) ckanzakura_KWZ_v1.0_vs_nr_noHit.fasta.gz
Cerasus x kanzakura v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) ckanzakura_KWZ_v1.0_vs_arabidopsis.xlsx.gz
Cerasus x kanzakura v1.0 proteins with arabidopsis (Araport11) (FASTA file) ckanzakura_KWZ_v1.0_vs_arabidopsis_hit.fasta.gz
Cerasus x kanzakura v1.0 proteins without arabidopsis (Araport11) (FASTA file) ckanzakura_KWZ_v1.0_vs_arabidopsis_noHit.fasta.gz
Cerasus x kanzakura v1.0 proteins with SwissProt homologs (EXCEL file) ckanzakura_KWZ_v1.0_vs_swissprot.xlsx.gz
Cerasus x kanzakura v1.0 proteins with SwissProt (FASTA file) ckanzakura_KWZ_v1.0_vs_swissprot_hit.fasta.gz
Cerasus x kanzakura v1.0 proteins without SwissProt (FASTA file) ckanzakura_KWZ_v1.0_vs_swissprot_noHit.fasta.gz
Cerasus x kanzakura v1.0 proteins with TrEMBL homologs (EXCEL file) ckanzakura_KWZ_v1.0_vs_trembl.xlsx.gz
Cerasus x kanzakura v1.0 proteins with TrEMBL (FASTA file) ckanzakura_KWZ_v1.0_vs_trembl_hit.fasta.gz
Cerasus x kanzakura v1.0 proteins without TrEMBL (FASTA file) ckanzakura_KWZ_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Cerasus x kanzakura KWZ Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) ckanzakura_KWZ_v1.0.fasta.gz
Repeats (GFF3 file) ckanzakura_KWZ_v1.0.repeats.gff3.gz

 

Gene Predictions

The Cerasus x kanzakura KWZ v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) ckanzakura_KWZ_v1.0.proteins.fasta.gz
CDS  (FASTA file) ckanzakura_KWZ_v1.0.cds.fasta.gz
Genes (GFF3 file) ckanzakura_KWZ_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Cerasus x kanzakura Kawazu-zakura 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).

Downloads

GO assignments from InterProScan ckanzakura_KWZ_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan ckanzakura_KWZ_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways ckanzakura_KWZ_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs ckanzakura_KWZ_v1.0_KEGG-pathways.xlsx.gz

 

Transcript Alignments
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.

 

Fragaria x ananassa GDR RefTrans v1 ckanzakura_KWZ_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 ckanzakura_KWZ_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 ckanzakura_KWZ_v1.0_p.persica_GDR_reftransV1
Rubus GDR RefTrans v2 ckanzakura_KWZ_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 ckanzakura_KWZ_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 ckanzakura_KWZ_v1.0_pyrus_GDR_reftransV1