Analysis Name | Lycium chinense Assembly & Annotation |
Sequencing technology | PacBio, Hi-C |
Assembly method | hifiasm (v 0.12) |
Release Date | 2022-11-22 |
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.
AbstractHyoscyamine 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 |
The Lycium chinense Assembly file is available in FASTA format.
Downloads
Chromosomes (FASTA file) | Lycium_chinense_genome_chromosomes.fa.gz |
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 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 |
Summary
Query | Chromosome | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
SLF15 | Chr09 | 102629097 | 2606536-2605280 | Solanum tuberosum DM8.1, SLF15 | 83.1 | F-box domain |
SLF12 | Chr09 | 102629097 | 29407372-29406219 | Solanum tuberosum DM8.1, SLF12 | 83.3 | F-box domain |
SLF4 | Chr09 | 102629097 | 68909419-68910579 | Petunia inflata KJ670477.1, S3-SLF4 | 80.9 | F-box domain |
SLF5 | Chr09 | 102629097 | 73943615-73942449 | Petunia hybrida AB933076.1, S0m-SLF5 | 82.0 | F-box domain |
Nucleotide
Protein