Prunus salicina Sanyueli FAAS Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus salicina Sanyueli FAAS Whole Genome v1.0 Assembly & Annotation
MethodNextDenovo
SourcePacBio and Illumina reads
Date performed2021-06-25

Publication

Manuscript submitted for publication.

Data submitted by Zhizhen Fang at Fujian Academy of Agricultural Sciences (FAAS), Chinese Academy of Agricultural Sciences (CAAS).

The previous version the ‘Sanyueli’ genome has been online in bioRxiv. Please see:Fang Z-Z, Lin-Wang K, Dai H, et al. The genome of low-chill Chinese plum ‘Sanyueli’ (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds. bioRxiv, 2020: 2020.2007.2031.193243. 

Name of the species and cultivar/accession 

Prunus salicina Sanyueli.  

Leaves for sequencing were collected from trees in the plum repository at the Fruit Research Institute of Fujian Academy of Agricultural Sciences (Jinan District, Fuzhou, Fujian province, China). 

Materials and Methods: some text to describe assembly and annotation process 

Plums are temperate fruit trees, which belong to the Prunus genus in the Rosaceae family, and have been grown throughout the world for centuries.Chinese plum (Prunus salicina Lindl.) plays an important role in the global production of plum.In this study, we report the genome sequence of the Chinese plum ‘Sanyueli’, which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in ‘Sanyueli’ revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of ‘Sanyueli’ was significantly lower than that in the dormant flower buds of the high chill requiring ‘Furongli’ plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of ‘Sanyueli’ plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum. 

Homology

Homology of the Prunus salicina Sanyueli FAAS 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 2018-05) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus salicina Sanyueli FAAS v1.0 proteins with NCBI nr homologs (EXCEL file) Psalicina_Sanyueli_FAAS_v1.0_vs_nr.xlsx.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with NCBI nr (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_nr_hit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins without NCBI nr (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_nr_noHit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Psalicina_Sanyueli_FAAS_v1.0_vs_arabidopsis.xlsx.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with arabidopsis (Araport11) (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins without arabidopsis (Araport11) (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with SwissProt homologs (EXCEL file) Psalicina_Sanyueli_FAAS_v1.0_vs_swissprot.xlsx.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with SwissProt (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_swissprot_hit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins without SwissProt (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_swissprot_noHit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with TrEMBL homologs (EXCEL file) Psalicina_Sanyueli_FAAS_v1.0_vs_trembl.xlsx.gz
Prunus salicina Sanyueli FAAS v1.0 proteins with TrEMBL (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_trembl_hit.fasta.gz
Prunus salicina Sanyueli FAAS v1.0 proteins without TrEMBL (FASTA file) Psalicina_Sanyueli_FAAS_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Prunus salicina Sanyueli FAAS Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Psalicina_Sanyueli_FAAS_v1.0.fasta.gz

 

Gene Predictions

The Prunus salicina Sanyueli FAAS v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences (FASTA file) Psalicina_Sanyueli_FAAS_v1.0.proteins.fasta.gz
CDS (FASTA file) Psalicina_Sanyueli_FAAS_v1.0.cds.fasta.gz
Gene sequences (FASTA file) Psalicina_Sanyueli_FAAS_v1.0.genes.fasta.gz
Genes (GFF3 file) Psalicina_Sanyueli_FAAS_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus salicina Sanyueli FAAS Genome v1.0 are available for download below. The Prunus salicina Sanyueli FAAS 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 Psalicina_Sanyueli_FAAS_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Psalicina_Sanyueli_FAAS_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Psalicina_Sanyueli_FAAS_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Psalicina_Sanyueli_FAAS_v1.0_KEGG-pathways.xlsx.gz