Articles
CHARACTERIZING THE GENOME OF WILD RELATIVES OF LIMNANTHES ALBA (MEADOWFOAM) USING MASSIVELY PARALLEL SEQUENCING
Article number
859_36
Pages
309 – 314
Language
English
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.
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.
Authors
S.C. Meyers, A. Liston
Keywords
Illumina, chloroplast genome, Limnanthes floccosa ssp. floccosa, Limnanthes floccosa ssp. grandiflora
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