Mandragora caulescens Assembly & Annotation

Overview

Analysis Name Mandragora caulescens 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) 756
Assembled genome size (Mb) 712
N50 of scaffolds (bp) 28,080,016
No. of contigs 808
N50 of contigs (bp) 25,262,060
GC content of the genome (%) 35.18
Anchored to chromosome (%) 94.67
Complete BUSCOs (%) 98.30
Assembly level Chromosome

Assembly

The Mandragora caulescens Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Mch.fasta.gz

Gene Predictions

The Mandragora caulescens genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Mch.Chr.gff.gz
CDS sequences (FASTA file) Mch_new.cds.fa.gz
Protein sequences (FASTA file) Mch_new.pep.fa.gz

Functional Analysis

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

Downloads

Domain from InterProScan Mandragora_caulescens.Pfam.tsv.gz

S genes

Summary

QueryChromosomeSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF18Chr10286710299671724-9672839Solanum tuberosum DM8.1, SLF18-283.7 F-box domain
SLF15Chr172526206018785245-18783980Solanum tuberosum DM8.1, SLF1584.0 F-box domain

Nucleotide

Protein

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