Abstract
Limnanthes (Limnanthaceae), commonly known as meadowfoam, has attracted attention in recent decades due to the novel physical and chemical characteristics of its seed oil. Currently, Limnanthes alba cultivars are grown on a limited scale in the United States where they have potential as a rotation crop in tandem with grass seed production. In order to characterize genetic variation within Limnanthes floccosa, a wild relative of Limnanthes alba, we sequenced genomic DNA from two individuals representing two subspecies. The samples were tagged with a 4 bp barcode, and duplexed in a single lane of the Illumina GAII and 710-730 Mb (~5 million, 76 bp paired end reads) were obtained per subspecies. Using a combination of de novo and reference guided sequence assembly, we obtained a complete 152.3 kbp chloroplast genome and 36 kbp of the mitochondrial genome from each L. floccosa subspecies. Using Limnanthes alba EST (12,248) and GSS (3662) sequences, we were able to compare over 1 Mb of the nuclear genome. These sequences were used to identify SNPs in the two subspecies, and demonstrate the ease and cost-effectiveness of obtaining large amounts of genomic data from wild relatives of cultivated species.
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Claims 6
Claim · model-written summary
Sequencing obtained 710-730 Mb per subspecies.
- Taxon
- Limnanthes floccosa
Limnanthes floccosat0 - Outcome
- obtained per subspeciese0
- Value
- 710-730 Mbe0
- Qualifier
- ~5 million, 76 bp paired end readse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The samples were tagged with a 4 bp barcode, and duplexed in a single lane of the Illumina GAII and 710-730 Mb (~5 million, 76 bp paired end reads) were obtained per subspecies.”
t0“Limnanthes floccosa, a wild relative”
Claim · model-written summary
A complete 152.3 kbp chloroplast genome was assembled from each subspecies.
- Taxon
- L. floccosaLimnanthes floccosae0
- Outcome
- chloroplast genomee0
- Value
- 152.3 kbpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Using a combination of de novo and reference guided sequence assembly, we obtained a complete 152.3 kbp chloroplast genome and 36 kbp of the mitochondrial genome from each L. floccosa subspecies.”
Claim · model-written summary
A 36 kbp mitochondrial genome sequence was obtained from each subspecies.
- Taxon
- L. floccosaLimnanthes floccosae0
- Outcome
- mitochondrial genomee0
- Value
- 36 kbpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Using a combination of de novo and reference guided sequence assembly, we obtained a complete 152.3 kbp chloroplast genome and 36 kbp of the mitochondrial genome from each L. floccosa subspecies.”
Claim · model-written summary
Over 1 Mb of nuclear genome was compared using L. alba sequences.
- Taxon
- Limnanthes albaLimnanthes albae0
- Outcome
- nuclear genomee0
- Value
- over 1 Mbe0
- Qualifier
- EST (12,248) and GSS (3662) sequencese0
Verbatim
e0“Using Limnanthes alba EST (12,248) and GSS (3662) sequences, we were able to compare over 1 Mb of the nuclear genome.”
Claim · model-written summary
The sequences enabled identification of SNPs in both subspecies.
- Taxon
- Limnanthes floccosaLimnanthes floccosat0
- Outcome
- SNPs in the two subspeciese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These sequences were used to identify SNPs in the two subspecies, and demonstrate the ease and cost-effectiveness of obtaining large amounts of genomic data from wild relatives of cultivated species.”
t0“Limnanthes floccosa, a wild relative”
Claim · model-written summary
The sequencing approach demonstrated ease and cost effectiveness for obtaining wild-relative genomic data.
- Taxon
- Limnanthes floccosaLimnanthes floccosat0
- Outcome
- ease and cost-effectiveness of obtaining large amounts of genomic datae0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These sequences were used to identify SNPs in the two subspecies, and demonstrate the ease and cost-effectiveness of obtaining large amounts of genomic data from wild relatives of cultivated species.”
t0“Limnanthes floccosa, a wild relative”