Skip to main content
SpringerLink
Log in

Identification and Evolutionary Analysis of FAD2 Gene Family in Green Plants

  • Published:
Tropical Plant Biology Aims and scope Submit manuscript

Abstract

Fatty acid desaturase 2 (FAD2) is a crucial enzyme in the biosynthesis of polyunsaturated fatty acids in plants, which introduce a double bond into oleic acid to produce linoleic acid. FAD2 is imperative to the application and nutritional value of vegetable oil as both oleic acid and linoleic acid are the primary constituent fatty acids and their relative proportion determines the nutritional value and oxidative stability in most temperate vegetable oils. In the study described herein, we have identified a total of 253 candidate FAD2 genes from the published genomes of 79 plants. Phylogenetic analysis showed that FAD2 genes in green plants can be divided into three categories, namely, eudicots, monocots and lower plants (except Amborella trichopoda). Through the analysis of its conserved domains, all FAD2 genes contain motifs harbouring HECGH, HRRHH and HVAHH, −the three histidine clusters that are important functional structures of FAD2 gene. According to exon/intron structure analysis, the number of introns varies greatly in lower plants. With the evolution of green plants, the number of introns decreases. This study found that introns were mainly located in the 5’UTR and CDs regions, and their length ranged from 4 bp to 11,233 BP. In addition, about 56% of the 3 ‘and 5’ ends of FAD2 are located at Ag: GT, and the total content of a and t is generally about 60%.Through other bioinformatics methods, we concluded that FAD2 was more conservative in the process of plant evolution. This study provides theoretical support for further analysis of FAD2 gene family evolution.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2):195–201

    Article  CAS  PubMed  Google Scholar 

  • Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2(2):28–36

    CAS  PubMed  Google Scholar 

  • Broun PS, Somerville C (1997) Accumulation of ricinoleic, lesquerolic, and densipolic acids in seeds of transgenic arabidopsis plants that express a fatty acyl hydroxylase cDNA from castor bean. Plant Physiol 113:933–942

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Broun P, Boddupalli S, Somerville C (2010) A bifunctional oleate 12-hydroxylase: desaturase from Lesquerella fendleri. Plant J 13:201–210

    Article  Google Scholar 

  • Cao SZX, Wood CC, Green AG, Singh SP, Liu L, Liu Q (2013) A large and functionally diverse family of Fad2 genes in safflower (Carthamus tinctorius L.). BMC Plant Biol 13:5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carlson KF (1992) Processing of oilseeds, fats, and oils international news on fats oils & related materials. INFORM 2:1034–1060

    Google Scholar 

  • Carlsson AS, Thomaeus S, Hamberg M, Stymne S (2010) Properties of two multifunctional plant fatty acid acetylenase/desaturase enzymes. Eur J Biochem 271:2991–2997

    Article  CAS  Google Scholar 

  • Chen C, Chen H, Zhang Y, Thomas HR, Xia R (2020) Tbtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13(8):1194–1202

    Article  CAS  PubMed  Google Scholar 

  • Dar AA, Choudhury AR, Kancharla PK, Neelakantan A (2017a) The FAD2 gene in plants: occurrence, regulation, and role. Front Plant Sci 8:1789

    Article  PubMed  PubMed Central  Google Scholar 

  • Dar AA, Choudhury AR, Kancharla PK, Neelakantan A (2017b) The FAD2 gene in plants: occurrence, regulation, and role. Front Plant Sci 8:1789

    Article  PubMed  PubMed Central  Google Scholar 

  • Dehghan Nayeri F, Yarizade K (2014) Bioinformatics study of delta-12 fatty acid desaturase 2 (FAD2) gene in oilseeds. Mol Biol Rep 41:5077–5087

    Article  CAS  PubMed  Google Scholar 

  • Dyer JM, Chapital DC, Kuan JCW, Mullen RT, Charlotta T, Mckeon TA, Pepperman AB (2002) Molecular analysis of a bifunctional fatty acid conjugase/desaturase from tung. Impl Evol Plant Fat Acid Divers Plant Physiol 130:2027–2038

    CAS  Google Scholar 

  • Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. https://doi.org/10.1186/1471-2105-5-113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012a) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186

    Article  CAS  PubMed  Google Scholar 

  • Goodstein DM et al. (2012b) Phytozome: a comparative platform for green plant genomics nucleic acids research: D1178-D1186

  • Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 30(Suppl 1):S162–S173

    Article  PubMed  Google Scholar 

  • Hazel JR, Williams EE (1990) The role of alterations in membrane lipid composition in enabling physiological adaptation of organisms to their physical environment. Prog Lipid Res 29:167–227

    Article  CAS  PubMed  Google Scholar 

  • HernNdez ML, Padilla MAN, Mancha M, Marti Nez-Rivas JM (2009) Expression analysis identifies FAD2-2 as the olive Oleate Desaturase gene mainly responsible for the linoleic acid content in virgin olive oil. J Agric Food Chem 57:6199–6206

    Article  CAS  Google Scholar 

  • Hoshino T, Takagi Y, Anai T (2010) Novel GmFAD2-1b mutant alleles created by reverse genetics induce marked elevation of oleic acid content in soybean seeds in combination with GmFAD2-1a mutant alleles. Breed Sci:60, 419–425

  • Iba K. (2006) Trienoic fatty acids and temperature tolerance of higher plants. In: Rai A.K., Takabe T. (eds) Abiotic stress tolerance in plants. Springer, Dordrecht. 978-1-4020-4388-8

    Google Scholar 

  • Jung KM, Heeja K, Jeong Sheop S, Chung-Han C, Ohlrogge JB, Chung SM (2006) Seed-specific expression of sesame microsomal oleic acid desaturase is controlled by combinatorial properties between negative cis-regulatory elements in the SeFAD2 promoter and enhancers in the 5'-UTR intron. Mol Genet Genom 276:351–368

    Article  CAS  Google Scholar 

  • Kachroo A, Kachroo P (2009) Fatty Acid-derived signals in plant defense. Annual Rev Phytopathol 47:153–176

    Article  CAS  Google Scholar 

  • Kinney AJ, Cahoon EB, Hitz WD (2002) Manipulating desaturase activities in transgenic crop plants. Biochem Soc Trans 30:1099

    Article  CAS  PubMed  Google Scholar 

  • Lee M, Lenman M, Banas A (1998) Identification of non-heme diiron proteins that catalyze triple bond and epoxy group formation. Science 280:915–918

    Article  CAS  PubMed  Google Scholar 

  • Lee KR et al. (2012) Molecular cloning and functional analysis of two FAD2 genes from American grape (Vitis labrusca L.) Gene 509

  • Li L, Wang X, Gai J, Yu D (2016) Molecular cloning and characterization of a novel microsomal oleate desaturase gene from soybean. J Plant Physiol 164:1516–1526

    Article  CAS  Google Scholar 

  • Liu Q, Brubaker CL, Green AG, Marshall DR, Sharp PJ, Singh SP (2001) Evolution of the FAD2-1 fatty acid desaturase 5' UTR intron and the molecular systematics of Gossypium (Malvaceae). Am J Bot 88(1):92–102

    Article  CAS  PubMed  Google Scholar 

  • Liu L, Xu W, Hu X, Liu H, Lin Y (2016) W-box and g-box elements play important roles in early senescence of rice flag leaf. Rep 6:20881

    CAS  Google Scholar 

  • Luisa MH (2009) Expression analysis identifies FAD2-2 as the olive oleate desaturase gene mainly responsible for the linoleic acid content in virgin olive oil. J Agr Food Chem 57(14):6199–6206

    Article  CAS  Google Scholar 

  • M C, Gill S, Hobbs D, Morgan C, Bancroft I (2003) Natural variation for seed oil composition in Arabidopsis thaliana. Phytochemistry 64:1077–1090

    Article  CAS  Google Scholar 

  • Marco B, Stefan B, Andrew W, Konstantin A, Gabriel S, Tobias S et al (2014) Swiss-model: modelling protein tertiary and quaternary structure using evolutionary information. Nuclc Acids Res 42(W1)

  • Mi JK, Kim JK, Shin JS, Mi CS (2007) The SebHLH transcription factor mediates trans-activation of the SeFAD2 gene promoter through binding to E- and G-box elements. Plant Mol Biol 64:453–466

    Article  CAS  Google Scholar 

  • Miquel M, James D, Dooner H, Browse J (1993) Arabidopsis requires polyunsaturated lipids for low-temperature survival. Proc NatL Acad Sci USA 90:6208–6212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohlrogge JB, Browse J, Somerville CR (1991) The genetics of plant lipids. Biochimica Et Biophysica Acta 1082:1–26

    Article  CAS  PubMed  Google Scholar 

  • Okuley J, Lightner J, Feldmann K, Yadav N (1994) Arabidopsis FAD2 gene encodes the enzyme that is essential for polyunsaturated lipid synthesis. Plant Cell 6:147–158

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pham AT, Lee JD, Shannon JG, Bilyeu KD (2010) Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait. Bmc Plant Biol 10:195

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pham AT, Lee JD, Shannon JG, Bilyeu KD (2011) A novel FAD2–1 A allele in a soybean plant introduction offers an alternate means to produce soybean seed oil with 85% oleic acid content. Theoretic Appl Genet 123:793–802

    Article  CAS  Google Scholar 

  • Pradeep K, Venugopal SC, Navarre DA, Ludmila L, Aardra K (2005) Role of salicylic acid and fatty acid desaturation pathways in ssi2-mediated signaling. Plant Physiol 139:1717–1735

    Article  CAS  Google Scholar 

  • Qing-Ming G, Srivathsa V, Duroy N, Aardra K (2011) Low oleic acid-derived repression of jasmonic acid-inducible defense responses requires the WRKY50 and WRKY51 proteins. Plant Physiol 155:464–476

    Article  CAS  Google Scholar 

  • Schlueter JA, Vasylenko-Sanders IF, Deshpande S, Yi J, Shoemaker RC (2007) The FAD2 gene family of soybean: insights into the structural and functional divergence of a paleopolyploid Genome Crop 47

  • Si-Wei Y, Xue-Long WU, Zhi-Hong L, Hong-Bing L, Rui-Zhi H (2012) Abiotic stresses and phytohormones regulate expression of FAD2 gene in Arabidopsis thaliana. J Integrative Agric:62–72

  • Smith TJ, Campbell RE, Drake MA (2016) Sensory properties of milk protein ingredients. Springer, New York, pp 197–223

    Google Scholar 

  • Somerville C, Browse J (1991) Plant lipids: metabolism. Mutants Membranes Sci 252:80–87

    CAS  Google Scholar 

  • Subudhi S, Kurdrid P, Hongsthong A, Sirijuntarut M, Cheevadhanarak S, Tanticharoen M (2008) Isolation and functional characterization of Spirulina D6D gene promoter: role of a putative GntR transcription factor in transcriptional regulation of D6D gene expression. Biochem Biophys Res Commun 365:643–649

    Article  CAS  PubMed  Google Scholar 

  • Tang GQ, Novitzky WP, Griffin HC, Huber SC, Dewey RE (2010) Oleate desaturase enzymes of soybean: evidence of regulation through differential stability and phosphorylation. Plant J 44:433–446

    Article  CAS  Google Scholar 

  • Timothy LB (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res Web Server issue 37(web server issue):W202–W208

    Google Scholar 

  • Vaishali K, Michael L (2003) The Structure and Early Evolution of Recently Arisen Gene Duplicates in the Caenorhabditis elegans. Genome Genet 165:1793–1803

    Google Scholar 

  • Van de Loo FJ, Broun P, Turner S, Somerville C (1995) An oleate 12-hydroxylase from Ricinus communis L. is a fatty acyl desaturase homolog. Proc Natl Acad Sci 92:6743–6747

  • Voinnet O, Rivas S, Mestre P, Baulcombe D (2003) Retracted: an enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. Plant J 33:949–956

    Article  CAS  PubMed  Google Scholar 

  • Wallis JG, Browse J (2002) Mutants of Arabidopsis reveal many roles for membrane lipids. Prog Lipid Res 41:254–278

    Article  CAS  PubMed  Google Scholar 

  • Wang TF, Ou Y, Guidotti G (1998) The Transmembrane domains of Ectoapyrase (CD39) affect its enzymatic activity and quaternary structure. J Biol Chem 273:24814–24821

    Article  CAS  PubMed  Google Scholar 

  • Wei D, Alessandro V, Fei C, Yue H, Zihua C, Liangsheng Z (2018) MORC domain definition and evolutionary analysis of the MORC gene family in Green plants. Genome Biol Evol 10:1730–1744

    Article  CAS  Google Scholar 

  • Yuan (2012) Abiotic stresses and Phytohormones regulate expression of FAD2 gene in Arabidopsis thaliana. J Integr Agr 11:62–72

  • Zhang J, Liu H, Sun J, Li B, Zhu Q, Chen S, Zhang H (2012) Arabidopsis fatty acid Desaturase FAD2 is required for salt tolerance during seed germination and early seedling growth. PLoS One 7(1):e30355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao M, Wang W, Wei L, Chen P, Peng L, Qin Z et al (2019) The evolution and biocatalysis of fad2 indicate its correlation to the content of seed oil in plants. Int J Mol Sci 20(4):849

    Article  CAS  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by NSFC (KAE16010A to S.C.; U1605212, 31761130074 to Y.Q.), a fund from Fujian Agriculture and Forestry University Forestry peak discipline construction project (71201800739).

Author information

Author notes

  1. Shijiang Cao and Jiashuo Zhang contributed equally to this work.

Authors and Affiliations

  1. College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China

    Shijiang Cao, Jiashuo Zhang, Hongwei Lv & Anqi Hu

  2. Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fuzhou, 350002, Fujian, China

    Shijiang Cao, Han Cheng, Mohammad Aslam, Mingliang Guo & Yuan Qin

  3. College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Han Cheng

  4. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China

    Mohammad Aslam & Yuan Qin

  5. College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Wei Dong

  6. College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Mingliang Guo

  7. Commonwealth Scientific and Industrial Research Organization Agriculture and Food, PO Box 1600, Canberra, ACT, 2601, Australia

    Qing Liu

Authors
  1. Shijiang Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiashuo Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Han Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mohammad Aslam
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hongwei Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anqi Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Mingliang Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Qing Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yuan Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuan Qin.

Ethics declarations

Conflict of Interest

The authors declare no conflict of interest.

Additional information

Communicated by: Yuval Cohen

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Table S1

(XLSX 19 kb)

Table S2

(XLSX 24 kb)

Figure S1

(PDF 60 kb)

Figure S2

(PDF 1106 kb)

Figure S3

(PDF 402 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cao, S., Zhang, J., Cheng, H. et al. Identification and Evolutionary Analysis of FAD2 Gene Family in Green Plants. Tropical Plant Biol. 14, 239–250 (2021). https://doi.org/10.1007/s12042-020-09276-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12042-020-09276-x

Keywords

Search

Navigation