| Analysis Name | Solanum sitiens 'LA1974 (cultivar)' ASM1680187v1 Assembly & Annotation |
| Sequencing technology | Illumina HiSeq; PacBio RSII; PacBio Sequel; BioNano Irys; 10x Genomics Chromium |
| Assembly method | MaSuRCA v. 3.2.2 |
| Release Date | 2021-02-02 |
Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Eerolla P, Spindlow DJ, Kashyap SP, Singh B, Prasanna H, Thompson AJ, Mohareb FR. De Novo Genome Assembly Of Solanum Sitiens Reveals Structural Variation Associated With Drought And Salinity Tolerance. Bioinformatics. 2021 Jan 30;37(14):1941–5. doi: 10.1093/bioinformatics/btab048.
AbstractMotivation: Solanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance.
Results: A high-quality de novo genome and transcriptome assembly for S. sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (∼159X coverage) and PacBio long reads (∼44X coverage), generating a total of ∼262 Gbp of DNA sequence. A reference genome of 1,245 Mbp, arranged in 1,483 scaffolds with a N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as beta-amylase 1 and YUCCA7.
Availability: S. sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI's Sequence Read Archive, under the BioProject number "PRJNA633104".All the commands and scripts necessary to generate the assembly are available at the following github repository: https://github.com/MCorentin/Solanum_sitiens_assembly.
Assembly statistics
| Genome size | 1.2 Gb |
| Number of scaffolds | 1,478 |
| Scaffold N50 | 1.8 Mb |
| Scaffold L50 | 186 |
| Number of contigs | 3,997 |
| Contig N50 | 844.5 kb |
| Contig L50 | 366 |
| Assembly level | Scaffold |
The Solanum sitiens 'LA1974 (cultivar)' ASM1680187v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_016801875.1_ASM1680187v1_genomic.fna.gz |
The Solanum sitiens 'LA1974 (cultivar)' ASM1680187v1 genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | - |
| Protein sequences (FASTA file) | - |
Functional annotation for the Solanum sitiens 'LA1974 (cultivar)' ASM1680187v1 is not available.
Downloads
| Domain from InterProScan | - |
Summary
| Query | Scaffold | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF11 | JABWTJ010000016.1 | 4721200 | 1398330-1397158 | Solanum pennellii NM_001323461.1, SLF11 | 97.5 | F-box domain |
| SLF16 | JABWTJ010000101.1 | 4371203 | 3439774-3440955 | Solanum lycopersicum SL2.31, SLF16 | 96.7 | F-box domain |
| SLF15 | JABWTJ010000101.1 | 4371203 | 4009713-4010972 | Solanum lycopersicum SL2.31, SLF15 | 95.6 | F-box domain |
| SLF7 | JABWTJ010000122.1 | 3524182 | 2100380-2101549 | Solanum peruvianum KJ814851.1, SLF7 | 96.8 | F-box domain |
| SLF6 | JABWTJ010000122.1 | 3524182 | 2221175-2222320 | Solanum lycopersicoides KU987626.1, SLF6 | 98.1 | F-box domain |
| SLF5 | JABWTJ010000122.1 | 3524182 | 2242634-2243803 | Solanum chilense KJ814884.1, SLF5 | 97.9 | F-box domain |
| SLF4 | JABWTJ010000122.1 | 3524182 | 2268140-2269306 | Solanum peruvianum KJ814848.1, SLF4 | 96.8 | F-box domain |
| SLF2 | JABWTJ010000137.1 | 1814728 | 233034-231847 | Solanum pennellii BK009231.1, SLF2 | 98.1 | F-box domain |
| SLF10Ψ | JABWTJ010000160.1 | 2138947 | 2023891-2025121 | Solanum chilense KJ814888.1, SLF10 | 94.8 | - |
| SLF5-2 | JABWTJ010000168.1 | 2118087 | 57472-58659 | Solanum lycopersicoides KU987627.2, SLF5 | 97.2 | F-box domain |
| SLF17 | JABWTJ010000199.1 | 2111152 | 569184-568003 | Solanum lycopersicoides KU960921.1, SLF17 | 96.4 | F-box domain |
| SLF22Ψ | JABWTJ010000209.1 | 1536909 | 854576-853450 | Solanum lycopersicoides KU960924.1, SLF22 | 99.4 | - |
| SLF9 | JABWTJ010000219.1 | 1342457 | 621184-620039 | Solanum lycopersicoides KU987631.1, SLF9 | 99.6 | F-box domain |
| SLF21 | JABWTJ010000251.1 | 1194399 | 321642-320332 | Solanum lycopersicoides KU960923.1, SLF21 | 99.6 | F-box domain |
| SLF6-2 | JABWTJ010000251.1 | 1194399 | 808296-809441 | Solanum lycopersicoides KU987626.1, SLF6 | 99.0 | F-box domain |
| SLF5-3 | JABWTJ010000251.1 | 1194399 | 837504-838673 | Solanum chilense KJ814884.1, SLF5 | 97.7 | F-box domain |
| SLF4-2 | JABWTJ010000251.1 | 1194399 | 892061-893224 | Solanum peruvianum KJ814848.1, SLF4 | 96.6 | F-box domain |
| SLF2-2 | JABWTJ010000251.1 | 1194399 | 1051318-1052505 | Solanum habrochaites KJ814908.1, SLF2-S1 | 97.1 | F-box domain |
| SLF20 | JABWTJ010000322.1 | 979256 | 587603-588769 | Solanum lycopersicoides KU960922.1, SLF20 | 99.5 | F-box domain |
| SLF6-3 | JABWTJ010000332.1 | 1277144 | 1075590-1076735 | Solanum tuberosum DM8.1, SLF6 | 91.8 | F-box domain |
| S-RNase | JABWTJ010000348.1 | 1340021 | 338583-338350,338263-337850 | Solanum tuberosum MZ561415.1, SRNase-S12 | 92.8 | Ribonuclease T2 family |
| SLF22-2 | JABWTJ010000382.1 | 1553066 | 393596-394729 | Solanum lycopersicoides KU960924.1, SLF22 | 99.4 | F-box domain |
| SLF3 | JABWTJ010000442.1 | 957390 | 855517-856680 | Solanum pennellii BK009230.1, SLF3 | 97.9 | F-box domain |
| SLF18 | JABWTJ010000458.1 | 665964 | 318027-319136 | Solanum lycopersicum SL2.31, SLF18 | 95.4 | F-box domain |
| SLF19 | JABWTJ010000458.1 | 665964 | 358640-357531 | Solanum lycopersicum SL2.31, SLF19 | 96.0 | F-box domain |
| SLF1Ψ | JABWTJ010000490.1 | 623224 | 477117-475947 | Solanum peruvianum KJ814846.1, SLF1 | 95.8 | - |
| SLF17-2 | JABWTJ010000745.1 | 705948 | 46693-47874 | Solanum lycopersicoides KU960921.1, SLF17 | 97.8 | F-box domain |
| SLF1-2 | JABWTJ010000757.1 | 317718 | 185148-186302 | Solanum peruvianum KJ814846.1, SLF1 | 94.8 | F-box domain |
| SLF23 | JABWTJ010000828.1 | 265193 | 102516-103673 | Solanum lycopersicoides KU960925.1, SLF23 | 98.7 | F-box domain |
| SLF7-2Ψ | JABWTJ010001027.1 | 161051 | 27713-26544 | Solanum peruvianum KJ814851.1, SLF7 | 97.2 | - |
| SLF20-2Ψ | JABWTJ010001043.1 | 153806 | 43558-42391 | Solanum lycopersicoides KU960922.1, SLF20 | 99.8 | - |
Nucleotide
Protein