Papaver armeniacum Yrk_Parm_ont_1 Assembly & Annotation

Overview

Analysis Name Papaver armeniacum Yrk_Parm_ont_1 Assembly & Annotation
Sequencing technology Oxford Nanopore PromethION
Assembly method FLYE version 2.8-b1674 v. 2019
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 3 Gb
Number of scaffolds 19,539
Scaffold N50 327.7 kb
Scaffold L50 2,485
Number of contigs 20,191
Contig N50 317.1 kb
Contig L50 2,549
Assembly level Scaffold

Assembly

The Papaver armeniacum Yrk_Parm_ont_1 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCA_023531295.1_Yrk_Parm_ont_1_genomic.fna.gz

Gene Predictions

The Papaver armeniacum Yrk_Parm_ont_1 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) GCA_023531295.1_Yrk_Parm_ont_1_genomic.gff.gz
CDS sequences (FASTA file) GCA_023531295.1_Yrk_Parm_ont_1_rna_from_genomic.fna.gz
Protein sequences (FASTA file) GCA_023531295.1_Yrk_Parm_ont_1_protein.faa.gz

Functional Analysis

Functional annotation for the Papaver armeniacum Yrk_Parm_ont_1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Papaver_armeniacum_Yrk_Parm_ont_1.Pfam.tsv.gz

S genes

Summary

QueryScaffoldSize(bp)CoordinatesBLASTn HitBLASTn %ID
S1-like-1JAJJWW010008662.1585453262826-263269Papaver somniferum XM_026603746.1, S1-like96.4
S1-like-2JAJJWW010008662.1585453308596-309066Papaver somniferum XM_026527103.1, S1-like96.4

Nucleotide

Protein

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