Brugmansia arborea Assembly & Annotation

Overview

Analysis Name Brugmansia arborea Assembly & Annotation
Sequencing technology PacBio, Hi-C
Assembly method hifiasm (v 0.12)
Release Date 2022-11-22
Reference Publication(s)

Yang J, Wu Y, Zhang P, Ma J, Yao YJ, Ma YL, Zhang L, Yang Y, Zhao C, Wu J, Fang X, Liu J. Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family. Nat Commun. 2023 Dec 20;14(1):8457. doi: 10.1038/s41467-023-44246-3.

Abstract

Hyoscyamine and scopolamine (HS), two valuable tropane alkaloids of significant medicinal importance, are found in multiple distantly related lineages within the Solanaceae family. Here we sequence the genomes of three representative species that produce HS from these lineages, and one species that does not produce HS. Our analysis reveals a shared biosynthetic pathway responsible for HS production in the three HS-producing species. We observe a high level of gene collinearity related to HS synthesis across the family in both types of species. By introducing gain-of-function and loss-of-function mutations at key sites, we confirm the reduced/lost or re-activated functions of critical genes involved in HS synthesis in both types of species, respectively. These findings indicate independent and repeated losses of the HS biosynthesis pathway since its origin in the ancestral lineage. Our results hold promise for potential future applications in the artificial engineering of HS biosynthesis in Solanaceae crops.

Assembly statistics

Estimated genome size (Mb) 1517
Assembled genome size (Mb) 1548
N50 of scaffolds (bp) 121,782,173
No. of contigs 1,398
N50 of contigs (bp) 7,701,694
GC content of the genome (%) 35.22
Anchored to chromosome (%) 97.40
Complete BUSCOs (%) 98.10
Assembly level Chromosome

Assembly

The Brugmansia arborea Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Brugmansia_arborea_genome_chromosomes.fa.gz

Gene Predictions

The Brugmansia arborea genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Brugmansia_arborea_genome_chromosomes.gff.gz
CDS sequences (FASTA file) Brugmansia_arborea_genome_chromosomes.cds.fa.gz
Protein sequences (FASTA file) Brugmansia_arborea_genome_chromosomes.pep.fa.gz

Functional Analysis

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

Downloads

Domain from InterProScan Brugmansia_arborea.Pfam.tsv.gz

S genes

Summary

QueryChromosomeSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF15Chr13663423604245499-4244222Solanum tuberosum DM8.1, SLF1585.6 F-box domain
S-RNaseChr136634236047234124-47233894,
47233776-47233357
Nicotiana alata U08861.1, NaS6-RNase87.1 Ribonuclease T2 family
SLF9Chr136634236055750558-55749410Solanum tuberosum DM8.1, SLF985.9 F-box domain
SLF2Chr136634236063782309-63783493Petunia hybrida, S5-SLF282.4 F-box domain

Nucleotide

Protein

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