Lycium chinense Assembly & Annotation

Overview

Analysis Name Lycium chinense 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) 1408
Assembled genome size (Mb) 1538
N50 of scaffolds (bp) 132,783,878
No. of contigs 1,406
N50 of contigs (bp) 2,994,494
GC content of the genome (%) 37.66
Anchored to chromosome (%) 98.53
Complete BUSCOs (%) 94.90
Assembly level Chromosome

Assembly

The Lycium chinense Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Lycium_chinense_genome_chromosomes.fa.gz

Gene Predictions

The Lycium chinense genome gene prediction files are available in GFF3 and FASTA format.

Downloads

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

Functional Analysis

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

Downloads

Domain from InterProScan Lycium_chinense.Pfam.tsv.gz

S genes

Summary

QueryChromosomeSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF15Chr091026290972606536-2605280Solanum tuberosum DM8.1, SLF1583.1 F-box domain
SLF12Chr0910262909729407372-29406219Solanum tuberosum DM8.1, SLF1283.3 F-box domain
SLF4Chr0910262909768909419-68910579Petunia inflata KJ670477.1, S3-SLF480.9 F-box domain
SLF5Chr0910262909773943615-73942449Petunia hybrida AB933076.1, S0m-SLF582.0 F-box domain

Nucleotide

Protein

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