Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 Assembly & Annotation

Overview

Analysis Name Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 Assembly & Annotation
Sequencing technology Illumina HiSeq
Assembly method SOAPdenovo v. MAY-2017
Release Date 2021-07-09
Reference Publication(s)

Yan L, Zhang Y, Cai G, Qing Y, Song J, Wang H, Tan X, Liu C, Yang M, Fang Z, Lai X. Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution. G3 (Bethesda). 2021 Sep 27;11(10):jkab262. doi: 10.1093/g3journal/jkab262

Abstract

Genetic diversity is the raw material for germplasm enhancement. Landraces and wild species relatives of potato, which contain a rich gene pool of valuable agronomic traits, can provide insights into the genetic diversity behind the adaptability of the common potato. The diploid plant, Solanum stenotomum (Sst), is believed to have an ancestral relationship with modern potato cultivars and be a potential source of resistance against disease. Sequencing of the Sst genome generated an assembly of 852.85 Mb (N50 scaffold size, 3.7 Mb). Pseudomolecule construction anchored 788.75 Mb of the assembly onto 12 pseudochromosomes, with an anchor rate of 92.4%. Genome annotation yielded 41,914 high-confidence protein-coding gene models and comparative analyses with closely related Solanaceae species identified 358 Sst-specific gene families, 885 gene families with expansion along the Sst lineage, and 149 genes experiencing accelerated rates of protein sequence evolution in Sst, the functions of which were mainly associated with defense responses, particularly against bacterial and fungal infection. Insights into the Sst genome and the genomic variation of cultivated potato taxa are valuable in elaborating the impact of potato evolution in early landrace diploid and facilitate modern potato breeding.

Assembly statistics

Genome size 846.2 Mb
Number of chromosomes 12
Number of scaffolds 17,083
Scaffold N50 62.6 Mb
Scaffold L50 6
Number of contigs 29,155
Contig N50 127.4 kb
Contig L50 1,679
Assembly level Chromosome

Assembly

The Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) GCF_019186545.1_ASM1918654v1_genomic.fna.gz

Gene Predictions

The Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) GCF_019186545.1_ASM1918654v1_genomic.gff.gz
CDS sequences (FASTA file) GCF_019186545.1_ASM1918654v1_cds_from_genomic.fna.gz
Protein sequences (FASTA file) GCF_019186545.1_ASM1918654v1_protein.faa.gz

Functional Analysis

Functional annotation for the Solanum stenotomum 'F172 (Isolate)' ASM1918654v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Solanum_stenotomum_F172_ASM1918654v1.Pfam.tsv.gz

S genes

Summary

QueryChromosomeSize(bp)CoordinatesBLASTn HitBLASTn %IDDomain
SLF13NC_064282.110465060435349119-35350324Solanum tuberosum DM8.1, SLF1398.8 F-box domain
SLF11ΨNC_064282.110465060437088682-37087533Solanum tuberosum DM8.1, SLF1193.9 -
SLF9NC_064282.110465060437939332-37940474Solanum tuberosum DM8.1, SLF998.5 F-box domain
SLF21NC_064282.110465060439063296-39064516Solanum tuberosum DM8.1, SLF2198.5 F-box domain
S-RNaseNC_064282.110465060439608518-39608291,
39608176-39607745
Solanum tuberosum MZ561408.1,
SRNase-S5
88.8 Ribonuclease T2 family
SLF5NC_064282.110465060440407843-40406674Solanum tuberosum DM8.1, SLF5-296.0 F-box domain
SLF7NC_064282.110465060440517286-40516114Solanum tuberosum DM8.1, SLF793.9 F-box domain
SLF12NC_064282.110465060441507598-41506432Solanum tuberosum DM8.1, SLF1297.9 F-box domain
SLF5-2NC_064282.110465060441517844-41519034Solanum tuberosum DM8.1, SLF595.9 F-box domain
SLF5-3ΨNC_064282.110465060442110144-42111326Solanum tuberosum DM8.1, SLF5-295.7 -
SLF4ΨNC_064282.110465060442176077-42177241Solanum pimpinellifolium
KJ814871.1, SLF4
94.0 -
SLF6ΨNC_064282.110465060442478344-42477205Solanum tuberosum DM8.1, SLF691.8 -
SLF19ΨNC_064282.110465060454613659-54614767Solanum tuberosum DM8.1, SLF1997.2 -
SLF18NC_064282.110465060454662328-54661213Solanum tuberosum DM8.1, SLF1897.4 F-box domain
SLF22NC_064282.110465060466318649-66317510Solanum tuberosum DM8.1, SLF2298.8 F-box domain
SLF23NC_064282.110465060467380803-67381960Solanum neorickii
MG266233.1, SLF23
94.4 F-box domain
SLF17NC_064282.110465060467452514-67453680Solanum tuberosum DM8.1, SLF1798.0 F-box domain
SLF16ΨNC_064282.110465060495267648-95268828Solanum tuberosum DM8.1, SLF1698.2 -
SLF15NC_064282.1104650604100652855-100654114Solanum tuberosum DM8.1, SLF1597.9 F-box domain

Nucleotide

Protein

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