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Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis.
BMC Genomics. 2015 Mar 24; 16:230.BG

Abstract

BACKGROUND

Castor oil is the only commercial source of hydroxy fatty acid that 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, and 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 hydroxy 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 will allow translation of 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 the quantitative PCR assay.

CONCLUSIONS

We have built a lesquerella seed transcriptome that provides a valuable reference in addition to the castor database for discovering genes involved in the synthesis of triacylglycerols enriched with hydroxy fatty acids. 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.

Authors+Show Affiliations

Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea. hukim64@korea.kr.U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, 800 Buchanan Street, Albany, CA, 94710, USA. grace.chen@ars.usda.gov.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25881190

Citation

Kim, Hyun Uk, and Grace Qianhong Chen. "Identification of Hydroxy Fatty Acid and Triacylglycerol Metabolism-related Genes in Lesquerella Through Seed Transcriptome Analysis." BMC Genomics, vol. 16, 2015, p. 230.
Kim HU, Chen GQ. Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis. BMC Genomics. 2015;16:230.
Kim, H. U., & Chen, G. Q. (2015). Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis. BMC Genomics, 16, 230. https://doi.org/10.1186/s12864-015-1413-8
Kim HU, Chen GQ. Identification of Hydroxy Fatty Acid and Triacylglycerol Metabolism-related Genes in Lesquerella Through Seed Transcriptome Analysis. BMC Genomics. 2015 Mar 24;16:230. PubMed PMID: 25881190.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of hydroxy fatty acid and triacylglycerol metabolism-related genes in lesquerella through seed transcriptome analysis. AU - Kim,Hyun Uk, AU - Chen,Grace Qianhong, Y1 - 2015/03/24/ PY - 2014/10/05/received PY - 2015/02/27/accepted PY - 2015/4/17/entrez PY - 2015/4/17/pubmed PY - 2016/1/21/medline SP - 230 EP - 230 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: Castor oil is the only commercial source of hydroxy fatty acid that 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, and 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 hydroxy 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 will allow translation of 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 the quantitative PCR assay. CONCLUSIONS: We have built a lesquerella seed transcriptome that provides a valuable reference in addition to the castor database for discovering genes involved in the synthesis of triacylglycerols enriched with hydroxy fatty acids. 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/25881190/Identification_of_hydroxy_fatty_acid_and_triacylglycerol_metabolism_related_genes_in_lesquerella_through_seed_transcriptome_analysis_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1413-8 DB - PRIME DP - Unbound Medicine ER -