Genomic data of Flax (Linum usitatissimum).
Dataset type: Genomic
Data released on March 07, 2014
Wang Z; Hobson N; Galindo L; Zhu S; Shi D; McDill J; Yang L; Hawkins S; Neutelings G; Datla R; Lambert G; Galbraith DW; Grassa CJ; Geraldes A; Cronk QC; Cullis C; Dash PK; Kumar PA; Cloutier S; Sharpe AG; Wong GK; Wang J; Deyholos MK (2014): Genomic data of Flax (Linum usitatissimum). GigaScience Database. https://doi.org/10.5524/100081
Flax (Linum usitatissimum) is also known as linseed. It is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds.
We sequenced the genome to a depth of approximately 69 X with short reads from a series of libraries with various insert sizes ( 300bp, 500bp, 2kb, 5kb and 10kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 25.9 Gb, with the contig and scaffold N50 values of 20.1 kb and 0.7 Mb respectively. We identified 43,484 protein-coding genes.
Additional details
Read the peer-reviewed publication(s):
- Wang, Z., Hobson, N., Galindo, L., Zhu, S., Shi, D., McDill, J., Yang, L., Hawkins, S., Neutelings, G., Datla, R., Lambert, G., Galbraith, D. W., Grassa, C. J., Geraldes, A., Cronk, Q. C., Cullis, C., Dash, P. K., Kumar, P. A., Cloutier, S., … Deyholos, M. K. (2012). The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. The Plant Journal, 72(3), 461–473. Portico. https://doi.org/10.1111/j.1365-313x.2012.05093.x (PubMed:22757964)
Accessions (data included in GigaDB):
BioProject: PRJNA68161
Click on a table column to sort the results.
Table Settings| Sample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
|---|---|---|---|---|---|
| SRS212314 | flax | Linum usitatissimum | Variety:CDC Bethune Geographic location (country and/or sea,region):no... Geographic location (latitude and longitude):not r... ... |
4006 |
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Table Settings| File Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
|---|---|---|---|---|---|---|---|---|
| Nucleotide FASTA format file of all gene coding sequences | Coding sequence | FASTA | 56.14 MB | 2014-03-07 | MD5 checksum: dd7ac943cce54dc8f681ea80b0fea6f8 |
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| Amino acid FASTA format file of all gene coding sequences | Protein sequence | FASTA | 20.93 MB | 2014-03-07 | MD5 checksum: af2b2617bb94d5ed2cd892427b11ab63 |
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| Gene coordinates information in GFF format. | Annotation | GFF | 34.19 MB | 2014-03-07 | MD5 checksum: b6fffe01fc1f35c50957cbe65154bc30 |
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| Nucleotide FASTA format file of the genomic assembly (Scaffolds) | Sequence assembly | FASTA | 319.24 MB | 2014-03-07 | MD5 checksum: bc2080c498ade3e07b013a1413c20480 |
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| Readme | UNKNOWN | 937 B | 2014-03-07 |
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