Author
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Chen, Grace |
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KIM, HUYN-UK - Korean Rural Development Administration |
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Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 2/27/2015 Publication Date: 3/24/2015 Citation: Chen, G.Q., Kim, H. 2015. Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis. Biomed Central (BMC) Genomics. 16:230 (21 p.) DOI 10.1186/s12864-015-1413-8. Interpretive Summary: Lesquerella (Physaria fendleri), a member of the Brassicaceae family, is currently being developed as a new industrial oilseed. Lesquerella is valued for its unusual hydroxy fatty acid (HFA) lesquerolic acid (20:1OH). The conventional source of HFA is ricinoleic acid (18:1OH) from castor oil. Ricinoleic acid and its derivatives are used as raw materials for numerous industrial products, such as lubricants, plasticizers and surfactants. The production of castor oil, however, is hampered by the presence of the toxin ricin and hyper-allergic 2S albumins in its seeds. Lesquerella, on the other hand, does not have such biologically toxic compounds, and thus its oil represents a safe source of HFA. As a step towards genetic engineering of lesquerella, we report an extensive survey of genes that are expressed in its seeds. This compilation will serve as a reference for the oilseed research community and facilitate identification of candidate genes that will provide genetic targets for seed quality improvement. Technical Abstract: Background: Castor oil is the only commercial source of hydroxy fatty acid which has industrial value. The production of castor oil is hampered by the presence of the toxin ricin in its seed. Lesquerella seed also accumulates hydroxy fatty acid and is free of ricin, thus it is being developed as a new crop for hydroxy fatty acid production. A high-throughput, large-scale sequencing of transcripts from developing lesquerella seeds was carried out by 454 pyrosequencing to generate a database for quality improvement of seed oil and other agronomic traits. Deep mining and characterization of acyl-lipid genes were conducted to uncover candidate genes for further studies of mechanisms underlying hydroxyl fatty acid and seed oil synthesis. Results: A total of 651 megabases of raw sequences from an mRNA sample of developing seeds was acquired. Bioinformatic analysis of these sequences revealed 59,914 transcripts representing 26,995 unique genes that include nearly all known seed expressed genes. Based on sequence similarity with known plant proteins, about 74% (19,861) genes matched with annotated coding genes. Among them 95% (18,868) showed highest sequence homology with Arabidopsis genes, which allows for translating genomics and genetics findings from Arabidopsis to lesquerella. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome assembly and identified 615 lesquerella genes involved in all known pathways of acyl-lipid metabolism. Further deep mining the transcriptome assembly led to identification of almost all lesquerella genes involved in fatty acid and triacylglycerol synthesis. Moreover, we characterized the spatial and temporal expression profiles of 15 key genes using quantitative PCR assay. Conclusions: We have built a lesquerella seed transcriptome which provides a valuable reference in addition to castor database for discovering genes involved in the synthesis of triacylglycerols enriched with hydroxy fatty acid. The information obtained from data mining and gene expression profiling will provide a resource not only for the study of hydroxy fatty acid metabolism, but also for the biotechnological production of hydroxy fatty acids in existing oilseed crops. |
