Papaver californicum Yrk_Pca_10X_1 Assembly & Annotation

Overview

Analysis Name Papaver californicum Yrk_Pca_10X_1 Assembly & Annotation
Sequencing technology Illumina NovaSeq
Assembly method supernova v. 2.0
Release Date 2022-05-23
Reference Publication(s)

Catania T, Li Y, Winzer T, Harvey D, Meade F, Caridi A, Leech A, Larson TR, Ning Z, Chang J, Van de Peer Y, Graham IA. A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago. Nat Commun. 2022 Jun 7;13(1):3150. doi: 10.1038/s41467-022-30856-w.

Abstract

The STORR gene fusion event is considered essential for the evolution of the promorphinan/morphinan subclass of benzylisoquinoline alkaloids (BIAs) in opium poppy as the resulting bi-modular protein performs the isomerization of (S)- to (R)-reticuline essential for their biosynthesis. Here, we show that of the 12 Papaver species analysed those containing the STORR gene fusion also contain promorphinans/morphinans with one important exception. P. californicum encodes a functionally conserved STORR but does not produce promorphinans/morphinans. We also show that the gene fusion event occurred only once, between 16.8-24.1 million years ago before the separation of P. californicum from other Clade 2 Papaver species. The most abundant BIA in P. californicum is (R)-glaucine, a member of the aporphine subclass of BIAs, raising the possibility that STORR, once evolved, contributes to the biosynthesis of more than just the promorphinan/morphinan subclass of BIAs in the Papaveraceae.

Assembly statistics

Genome size 1.4 Gb
Number of scaffolds 34,741
Scaffold N50 4.4 Mb
Scaffold L50 78
Number of contigs 64,186
Contig N50 65 kb
Contig L50 5,750
Assembly level Scaffold

Assembly

The Papaver californicum Yrk_Pca_10X_1 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_023531435.1_Yrk_Pca_10X_1_genomic.fna.gz

Gene Predictions

The Papaver californicum Yrk_Pca_10X_1 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) GCA_023531435.1_Yrk_Pca_10X_1_genomic.gff.gz
CDS sequences (FASTA file) GCA_023531435.1_Yrk_Pca_10X_1_rna_from_genomic.fna.gz
Protein sequences (FASTA file) GCA_023531435.1_Yrk_Pca_10X_1_protein.faa.gz

Functional Analysis

Functional annotation for the Papaver californicum Yrk_Pca_10X_1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Papaver_californicum_Yrk_Pca_10X_1.Pfam.tsv.gz

S genes

Summary

QueryScaffoldSize(bp)CoordinatesBLASTn HitBLASTn %ID
S1-likeJAJJMC010003991.11763753714263653-14263105Papaver somniferum XM_026594847.1, S1-like91.139

Nucleotide

Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences