| Analysis Name | Nicotiana otophora Noto Assembly & Annotation |
| Sequencing technology | Illumina HiSeq |
| Assembly method | SOAPdenovo v. 1.05 |
| Release Date | 2014-06-05 |
Sierro N, Battey JN, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV. The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun. 2014 May 8;5:3833. doi: 10.1038/ncomms4833.
AbstractThe allotetraploid plant Nicotiana tabacum (common tobacco) is a major crop species and a model organism, for which only very fragmented genomic sequences are currently available. Here we report high-quality draft genomes for three main tobacco varieties. These genomes show both the low divergence of tobacco from its ancestors and microsynteny with other Solanaceae species. We identify over 90,000 gene models and determine the ancestral origin of tobacco mosaic virus and potyvirus disease resistance in tobacco. We anticipate that the draft genomes will strengthen the use of N. tabacum as a versatile model organism for functional genomics and biotechnology applications.
Assembly statistics
| Genome size | 2.7 Gb |
| Number of scaffolds | 929,607 |
| Scaffold N50 | 26.6 kb |
| Scaffold L50 | 18,061 |
| Number of contigs | 1,121,520 |
| Contig N50 | 11.3 kb |
| Contig L50 | 44,787 |
| Assembly level | Scaffold |
The Nicotiana otophora Noto Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_000715115.1_Noto_genomic.fna.gz |
The Nicotiana otophora Noto genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | - |
| Protein sequences (FASTA file) | - |
Functional annotation for the Nicotiana otophora Noto is not available.
Downloads
| Domain from InterProScan | - |
Summary
| Query | Scaffold | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF-1 | AWOL01S0008085.1 | 112210 | 39909-38731 | Nicotiana alata EF420256.1, NaDD6-S2 | 92.6 | F-box domain |
| SLF-2 | AWOL01S0009934.1 | 119699 | 54847-56016 | Nicotiana alata EF420255.1, NaDD5-S2 | 87.7 | F-box domain |
| SLF-3 | AWOL01S0013543.1 | 24873 | 18077-19252 | Nicotiana alata EF420253.1, NaDD3-S1 | 89.8 | F-box domain |
| S-RNase | AWOL01S0016020.1 | 154175 | 60399-60635,60749-61177 | Solanum tuberosum MZ561409.1, SRNase-S6 | 81.6 | Ribonuclease T2 family |
| SLF-4 | AWOL01S0016020.1 | 154175 | 103627-102485 | Nicotiana alata EF420253.1, NaDD3-S1 | 90.0 | F-box domain |
| SLF-5 | AWOL01S0026916.1 | 147178 | 134176-135345 | Nicotiana alata EF420255.1, NaDD5-S2 | 89.0 | F-box domain |
| S-RNase-2 | AWOL01S0045891.1 | 62207 | 54073-54312,54414-54842 | Petunia inflata M67990.2, PiS1-RNase | 86.4 | Ribonuclease T2 family |
Nucleotide
Protein