Prunus avium Tieton Genome v2.0 Assembly & Annotation

Overview
Analysis NamePrunus avium Tieton Genome v2.0 Assembly & Annotation
MethodNECAT, medaka and nextPolish (na)
SourceALLHiC and HiC
Date performed2020-09-29

Publication:

Wang J, Liu W, Zhu D, Hong P, Zhang S, Xiao S, Tan Y, Chen X, Xu L, Zong X, Zhang L, Wei H, Yuan X, Liu Q. Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing.. Horticulture research. 2020; 7:122.

Overview:

Sweet cherry (Prunus avium) is an economically significant fruit species in the genus Prunus. However, in contrast to other important fruit trees in this genus, only one draft genome assembly is available for sweet cherry, which was assembled using only Illumina short-read sequences. The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies. A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed. A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated, representing ~190x and 136x coverage, respectively, of the sweet cherry genome. The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb. Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59% of the bases in the assembled genome. Genome annotation revealed that more than half of the genome (59.40%) was composed of repetitive sequences, and 40,338 protein-coding genes were predicted, 75.40% of which were functionally annotated. With the chromosome-scale assembly, we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry. Four auxin-responsive genes (two GH3s and two SAURs) were induced in the late stage of fruit development, indicating that auxin is crucial for the sweet cherry ripening process. In addition, 772 resistance genes were identified and functionally predicted in the sweet cherry genome. The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.

 

Homology Analysis

Homology of the Prunus avium Tieton genome v2.0 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 avium Tieton v2.0 proteins with NCBI nr homologs (EXCEL file) Pa_Tieton_v2.0_vs_nr.xlsx.gz
Prunus avium Tieton v2.0 proteins with NCBI nr (FASTA file) Pa_Tieton_v2.0_vs_nr_hit.fasta.gz
Prunus avium Tieton v2.0 proteins without NCBI nr (FASTA file) Pa_Tieton_v2.0_vs_nr_noHit.fasta.gz
Prunus avium Tieton v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pa_Tieton_v2.0_vs_arabidopsis.xlsx.gz
Prunus avium Tieton v2.0 proteins with arabidopsis (Araport11) (FASTA file) Pa_Tieton_v2.0_vs_arabidopsis_hit.fasta.gz
Prunus avium Tieton v2.0 proteins without arabidopsis (Araport11) (FASTA file) Pa_Tieton_v2.0_vs_arabidopsis_noHit.fasta.gz
Prunus avium Tieton v2.0 proteins with SwissProt homologs (EXCEL file) Pa_Tieton_v2.0_vs_swissprot.xlsx.gz
Prunus avium Tieton v2.0 proteins with SwissProt (FASTA file) Pa_Tieton_v2.0_vs_swissprot_hit.fasta.gz
Prunus avium Tieton v2.0 proteins without SwissProt (FASTA file) Pa_Tieton_v2.0_vs_swissprot_noHit.fasta.gz
Prunus avium Tieton v2.0 proteins with TrEMBL homologs (EXCEL file) Pa_Tieton_v2.0_vs_trembl.xlsx.gz
Prunus avium Tieton v2.0 proteins with TrEMBL (FASTA file) Pa_Tieton_v2.0_vs_trembl_hit.fasta.gz
Prunus avium Tieton v2.0 proteins without TrEMBL (FASTA file) Pa_Tieton_v2.0_vs_trembl_noHit.fasta.gz

 

Download

All assembly and annotation files are available for download by selecting the desired data type in the left-hand side bar.  Each data type page will provide a description of the available files and links to download.

Assembly

The Prunus avium Tieton Genome v2.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Prunus_avium_Tieton.v2.0.fasta.gz
Repeats (GFF3 file) Prunus_avium_Tieton.v2.0.repeats.gff3.gz

 

Gene Predictions

The Prunus avium Tieton v2.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Prunus_avium_Tieton.v2.0.proteins.fasta.gz
Tanscript sequences (FASTA file) Prunus_avium_Tieton.v2.0.transcripts.fasta.gz
Genes (GFF3 file) Prunus_avium_Tieton.v2.0.genes.gff3.gz
Functional Analysis

Functional annotation for the Prunus avium Tieton genome v2.0 are available for download below. The Prunus avium Tieton genome v2.0 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 Pa_Tieton_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Pa_Tieton_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Pa_Tieton_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Pa_Tieton_v2.0_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 Prunus avium Tieton genome v2.0 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 Prunus avium Tieton _v2.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus avium Tieton _v2.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus avium Tieton _v2.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus avium Tieton _v2.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus avium Tieton _v2.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus avium Tieton _v2.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus avium Tieton _v2.0_rubus_GDR_reftransV2