Polyploid genome of Camelina sativarevealed by isolation of fatty acid synthesis genes

Abstract

BackgroundCamelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD) 2 and fatty acid elongase (FAE) 1, which revealed unexpected complexity in the C. sativa genome.ResultsIn C. sativa, Southern analysis indicates the presence of three copies of both FAD2 and FAE1 as well as LFY, a known single copy gene in other species. All three copies of both CsFAD2 and CsFAE1 are expressed in developing seeds, and sequence alignments show that previously described conserved sites are present, suggesting that all three copies of both genes could be functional. The regions downstream of CsFAD2 and upstream of CsFAE1 demonstrate co-linearity with the Arabidopsis genome. In addition, three expressed haplotypes were observed for six predicted single-copy genes in 454 sequencing analysis and results from flow cytometry indicate that the DNA content of C. sativa is approximately three-fold that of diploid Camelina relatives. Phylogenetic analyses further support a history of duplication and indicate that C. sativa and C. microcarpa might share a parental genome.ConclusionsThere is compelling evidence for triplication of the C. sativa genome, including a larger chromosome number and three-fold larger measured genome size than other Camelina relatives, three isolated copies of FAD2, FAE1, and the KCS17-FAE1 intergenic region, and three expressed haplotypes observed for six predicted single-copy genes. Based on these results, we propose that C. sativa be considered an allohexaploid. The characterization of fatty acid synthesis pathway genes will allow for the future manipulation of oil composition of this emerging biofuel crop; however, targeted manipulations of oil composition and general development of C. sativa should consider and, when possible take advantage of, the implications of polyploidy.

Selective gene dosage by CRISPR‐Cas9 genome editing in hexaploid Camelina sativa

“…Céline, CsFAD2‐1, CsFAD2‐2 and CsFAD2‐3 showed they should also be targeted (Hutcheon et al ., 2010; Kang et al ., 2011). The sgRNA sequences were chosen based on the following: (i) TEFOR specificity score, (ii) the absence of predicted off‐target sites, including up to 4 mismatches (even near the PAM), (iii) their presence in the first half of the coding sequence and (iv) the strict sequence conservation within the three CsFAD2 genes (Figures S1A‐B and S2).…”

Two Acyltransferases Contribute Differently to Linolenic Acid Levels in Seed Oil

“…S3). Since C. sativa has a hexaploid genome (Hutcheon et al, 2010;Kagale et al, 2014), all genes may occur in up to three copies. It should be noted that, due to the high homology between genes in the subgenomes, neither the amiRNAs nor the primers used for this qRT-PCR experiment could distinguish between these different copies.…”

Phosphatidic Acid Binds to Cytosolic Glyceraldehyde-3-phosphate Dehydrogenase and Promotes Its Cleavage in Arabidopsis

“…These proteins were sequenced by mass spectrometry. Because the Camelina genome has not been fully sequenced, the protein sequences were blasted against the Arabidopsis data base based on genetic similarity between the two closely related plant species (Ͼ90% in genomic identity) (34).…”