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Evolution of the KCS gene family in plants: the history of gene duplication, sub/neofunctionalization and redundancy


Very long-chain fatty acids (VLCFAs) play an important role in the survival and development of plants, and VLCFA synthesis is regulated by β-ketoacyl-CoA synthases (KCSs), which catalyze the condensation of an acyl-CoA with malonyl-CoA. Here, we present a genome-wide survey of the genes encoding these enzymes, KCS genes, in 28 species (26 genomes and two transcriptomes), which represents a large phylogenetic scale, and also reconstruct the evolutionary history of this gene family. KCS genes were initially single-copy genes in the green plant lineage; duplication resulted in five ancestral copies in land plants, forming five fundamental monophyletic groups in the phylogenetic tree. Subsequently, KCS genes duplicated to generate 11 genes of angiosperm origin, expanding up to 20–30 members in further-diverged angiosperm species. During this process, tandem duplications had only a small contribution, whereas polyploidy events and large-scale segmental duplications appear to be the main driving force. Accompanying this expansion were variations that led to the sub- and neofunctionalization of different members, resulting in specificity that is likely determined by the 3-D protein structure. Novel functions involved in other physiological processes emerged as well, though redundancy is also observed, largely among recent duplications. Conserved sites and variable sites of KCS proteins are also identified by statistical analysis. The variable sites are likely to be involved in the emergence of product specificity and catalytic power, and conserved sites are possibly responsible for the preservation of fundamental function.

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  1. Amborella-Genome-Project (2013) The Amborella genome and the evolution of flowering plants. Science 342:1241089

  2. Ameline-Torregrosa C, Wang BB, O’Bleness MS, Deshpande S, Zhu H, Roe B, Young ND, Cannon SB (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146:5–21

  3. Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60:685–699

  4. Aya K, Kobayashi M, Tanaka J, Ohyanagi H, Suzuki T, Yano K, Takano T, Matsuoka M (2015) De novo transcriptome assembly of a fern, Lygodium japonicum, and a web resource database, Ljtrans DB. Plant Cell Physiol 56:e5

  5. Blacklock BJ, Jaworski JG (2006) Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases. Biochem Biophys Res Commun 346:583–590

  6. Cahoon EB, Marillia EF, Stecca KL, Hall SE, Taylor DC, Kinney AJ (2000) Production of fatty acid components of meadowfoam oil in somatic soybean embryos. Plant Physiol 124:243–251

  7. Costaglioli P, Joubes J, Garcia C, Stef M, Arveiler B, Lessire R, Garbay B (2005) Profiling candidate genes involved in wax biosynthesis in Arabidopsis thaliana by microarray analysis. Biochim Biophys Acta 1734:247–258

  8. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190

  9. Dufton MJ (1986) Genetic code redundancy and its differential influence on the evolution of protein interiors versus exteriors. J Theor Biol 122:231–236

  10. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

  11. Eiamsa-Ard P, Kanjana-Opas A, Cahoon EB, Chodok P, Kaewsuwan S (2013) Two novel Physcomitrella patens fatty acid elongases (ELOs): identification and functional characterization. Appl Microbiol Biotechnol 97:3485–3497

  12. Fehling E, Mukherjee KD (1991) Acyl-CoA elongase from a higher plant (Lunaria annua): metabolic intermediates of very-long-chain acyl-CoA products and substrate specificity. Biochim Biophys Acta 1082:239–246

  13. Fiebig A, Mayfield JA, Miley NL, Chau S, Fischer RL, Preuss D (2000) Alterations in CER6, a gene identical to CUT1, differentially affect long-chain lipid content on the surface of pollen and stems. Plant Cell 12:2001–2008

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

  15. Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224

  16. Gray JE, Holroyd GH, van der Lee FM, Bahrami AR, Sijmons PC, Woodward FI, Schuch W, Hetherington AM (2000) The HIC signalling pathway links CO2 perception to stomatal development. Nature 408:713–716

  17. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704

  18. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

  19. Haslam TM, Kunst L (2013) Extending the story of very-long-chain fatty acid elongation. Plant Sci 210:93–107

  20. Haslam TM, Manas-Fernandez A, Zhao L, Kunst L (2012) Arabidopsis ECERIFERUM2 is a component of the fatty acid elongation machinery required for fatty acid extension to exceptional lengths. Plant Physiol 160:1164–1174

  21. Haslam TM, Haslam R, Thoraval D, Pascal S, Delude C, Domergue F, Fernandez AM, Beaudoin F, Napier JA, Kunst L, Joubes J (2015) ECERIFERUM2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation. Plant Physiol 167:682–692

  22. Jakobsson A, Westerberg R, Jacobsson A (2006) Fatty acid elongases in mammals: their regulation and roles in metabolism. Prog Lipid Res 45:237–249

  23. James DW Jr, Dooner HK (1990) Isolation of EMS-induced mutants in Arabidopsis altered in seed fatty acid composition. Theor Appl Genet 80:241–245

  24. James DW, Lim E, Keller J, Plooy I, Ralston E, Dooner HK (1995) Direct tagging of the Arabidopsis FATTY ACID ELONGATION1 (FAE1) gene with the maize transposon Activator. Plant Cell 7:309–319

  25. Jasinski S, Lecureuil A, Miquel M, Loudet O, Raffaele S, Froissard M, Guerche P (2012) Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in Arabidopsis thaliana. PLoS One 7:e49261

  26. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100

  27. Joubes J, Raffaele S, Bourdenx B, Garcia C, Laroche-Traineau J, Moreau P, Domergue F, Lessire R (2008) The VLCFA elongase gene family in Arabidopsis thaliana: phylogenetic analysis, 3D modelling and expression profiling. Plant Mol Biol 67:547–566

  28. Ju CL, Van de Poel B, Cooper ED, Thierer JH, Gibbons TR, Delwiche CF, CC R (2015) Conservation of ethylene as a plant hormone over 450 million years of evolution. Nat Plants 14004:1–7

  29. Kajikawa M, Yamaoka S, Yamato KT, Kanamaru H, Sakuradani E, Shimizu S, Fukuzawa H, Ohyama K (2003a) Functional analysis of a beta-ketoacyl-CoA synthase gene, MpFAE2, by gene silencing in the liverwort Marchantia polymorpha L. Biosci Biotechnol Biochem 67:605–612

  30. Kajikawa M, Yamato KT, Kanamaru H, Sakuradani E, Shimizu S, Fukuzawa H, Sakai Y, Ohyama K (2003b) MpFAE3, a beta-ketoacyl-CoA synthase gene in the liverwort Marchantia polymorpha L., is preferentially involved in elongation of palmitic acid to stearic acid. Biosci Biotechnol Biochem 67:1667–1674

  31. Kim J, Jung JH, Lee SB, Go YS, Kim HJ, Cahoon R, Markham JE, Cahoon EB, Suh MC (2013) Arabidopsis 3-ketoacyl-coenzyme a synthase9 is involved in the synthesis of tetracosanoic acids as precursors of cuticular waxes, suberins, sphingolipids, and phospholipids. Plant Physiol 162:567–580

  32. Kunst L, Taylor DC, UE W (1992) Fatty acid elongation in developing seeds of Arabidopsis thaliana. Plant Physiol Biochem 30:425–434

  33. Lassner MW, Lardizabal K, Metz JG (1996) A jojoba beta-Ketoacyl-CoA synthase cDNA complements the canola fatty acid elongation mutation in transgenic plants. Plant Cell 8:281–292

  34. Lechelt-Kunze C, Meissner RC, Drewes M, Tietjen K (2003) Flufenacet herbicide treatment phenocopies the fiddlehead mutant in Arabidopsis thaliana. Pest Manag Sci 59:847–856

  35. Lee SB, Jung SJ, Go YS, Kim HU, Kim JK, Cho HJ, Park OK, Suh MC (2009) Two Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynthesis, but differentially controlled by osmotic stress. Plant J 60:462–475

  36. Lee TH, Tang H, Wang X, Paterson AH (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res 41:D1152–D1158

  37. Lemieux B, Miquel M, Somerville C, Browse J (1990) Mutants of Arabidopsis with alterations in seed lipid fatty acid composition. Theor Appl Genet 80:234–240

  38. Lewis LA, McCourt RM (2004) Green algae and the origin of land plants. Am J Bot 91:1535–1556

  39. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245–250

  40. Mietkiewska E, Giblin EM, Wang S, Barton DL, Dirpaul J, Brost JM, Katavic V, Taylor DC (2004) Seed-specific heterologous expression of a nasturtium FAE gene in Arabidopsis results in a dramatic increase in the proportion of erucic acid. Plant Physiol 136:2665–2675

  41. Nowak MA, Boerlijst MC, Cooke J, Smith JM (1997) Evolution of genetic redundancy. Nature 388:167–171

  42. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hallman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Kaller M, Luthman J, Lysholm F, Niittyla T, Olson A, Rilakovic N, Ritland C, Rossello JA, Sena J, Svensson T, Talavera-Lopez C, Theissen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584

  43. Oh CS, Toke DA, Mandala S, Martin CE (1997) ELO2 and ELO3, homologues of the Saccharomyces cerevisiae ELO1 gene, function in fatty acid elongation and are required for sphingolipid formation. J Biol Chem 272:17376–17384

  44. Paul S, Gable K, Beaudoin F, Cahoon E, Jaworski J, Napier JA, Dunn TM (2006) Members of the Arabidopsis FAE1-like 3-ketoacyl-CoA synthase gene family substitute for the Elop proteins of Saccharomyces cerevisiae. J Biol Chem 281:9018–9029

  45. Post-Beittenmiller D (1996) Biochemistry and molecular biology of wax production in plants. Annu Rev Plant Physiol Plant Mol Biol 47:405–430

  46. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329:223–226

  47. Qiu YL, Cho Y, Cox JC, Palmer JD (1998) The gain of three mitochondrial introns identifies liverworts as the earliest land plants. Nature 394:671–674

  48. Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M, Zimmer EA, Chen Z, Savolainen V, Chase MW (1999) The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404–407

  49. Shao ZQ, Zhang YM, Hang YY, Xue JY, Zhou GC, Wu P, Wu XY, Wu XZ, Wang Q, Wang B, Chen JQ (2014) Long-term evolution of nucleotide-binding site-leucine-rich repeat genes: understanding gained from and beyond the legume family. Plant Physiol 166:217–234

  50. Stevens P (2015) Angiosperm Phylogeny Website. In: Version 14 edn, St Louis.

  51. Stolzer M, Lai H, Xu M, Sathaye D, Vernot B, Durand D (2012) Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28:i409–i415

  52. Sun XQ, Pang H, Guo JL, Peng B, Bai MM, Hang YY (2011) Fatty acid analysis of the seed oil in a germplasm collection of 94 species in 58 genera of Brassicaceae. Chem Ind For Prod 31:46

  53. Sun X, Pang H, Li M, Peng B, Guo H, Yan Q, Hang Y (2013) Evolutionary pattern of the FAE1 gene in brassicaceae and its correlation with the erucic acid trait. PLoS One 8:e83535

  54. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

  55. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

  56. Toke DA, Martin CE (1996) Isolation and characterization of a gene affecting fatty acid elongation in Saccharomyces cerevisiae. J Biol Chem 271:18413–18422

  57. Trenkamp S, Martin W, Tietjen K (2004) Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides. Proc Natl Acad Sci USA 101:11903–11908

  58. Tresch S, Heilmann M, Christiansen N, Looser R, Grossmann K (2012) Inhibition of saturated very-long-chain fatty acid biosynthesis by mefluidide and perfluidone, selective inhibitors of 3-ketoacyl-CoA synthases. Phytochemistry 76:162–171

  59. Vavouri T, Semple JI, Lehner B (2008) Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution. Trends Genet 24:485–488

  60. Wagner A (1996) Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators. Biol Cybern 74:557–567

  61. Wang B, Xue J, Li L, Liu Y, Qiu YL (2009) The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr Genet 55:601–609

  62. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40:e49

  63. Wodniok S, Brinkmann H, Glockner G, Heidel AJ, Philippe H, Melkonian M, Becker B (2011) Origin of land plants: do conjugating green algae hold the key? BMC Evol Biol 11:104

  64. Wu P, Shao ZQ, Wu XZ, Wang Q, Wang B, Chen JQ, Hang YY, Xue JY (2014) Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa. Gene 540:54–61

  65. Xue JY, Liu Y, Li L, Wang B, Qiu YL (2010) The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr Genet 56:53–61

  66. Xue JY, Wang Y, Wu P, Wang Q, Yang LT, Pan XH, Wang B, Chen JQ (2012) A primary survey on bryophyte species reveals two novel classes of nucleotide-binding site (NBS) genes. PLoS One 7:e36700

  67. Zeng L, Zhang Q, Sun R, Kong H, Zhang N, Ma H (2014) Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun 5:4956

  68. Zhang H, Miao H, Wang L, Qu L, Liu H, Wang Q, Yue M (2013) Genome sequencing of the important oilseed crop Sesamum indicum L. Genome Biol 14:401

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We gratefully acknowledge the editor-in-chief Dr. Hohmann and two anonymous reviewers for their constructive suggestions to improve the manuscript, Dr. Zhu-Qing Shao at Nanjing University for his assistance in the bioinformatics analysis, and Dr. Yang Liu at the University of Connecticut for insightful discussions. This work was supported by grants from the National Natural Science Founding of China to JYX (31300190), XQS (31200177 and 31470448), the Natural Science Founding of Jiangsu Province (BK20130565) to JYX, and Funds of Jiangsu Province Key Laboratory for Plant Ex Situ Conservation to XQS (QIAN201202) (,, The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Correspondence to Yue-Yu Hang or Jia-Yu Xue.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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H.-S. Guo and Y.-M. Zhang contributed equally to this work.

Communicated by S. Hohmann.

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Figure S1. The detailed phylogenetic tree of KCS genes. Five monophyletic land plant groups, A (red), B (light blue), C (orange), D (dark blue) and E (black) and 11 angiosperm groups (1–11) are indicated. The scale bars represent numbers of amino acid substitutions per site. The support values (SH-aLRT value) for basal nodes are indicated. Figure S2. The amino acid frequencies of KCS proteins (by WebLogo). Table S1. The positions and corresponding amino acids with frequencies >90 %, >70 % and >50 % among the whole gene family. Table S2. The tandem arrayed KCS genes among the surveyed plant genomes (PDF 8466 kb)

Table S3. The identity and divergence of KCS proteins. Percent identities are in presented in upper triangle; percent divergences are presented in lower triangle; potential redundant genes are highlighted in red (XLSX 92 kb)

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Guo, H., Zhang, Y., Sun, X. et al. Evolution of the KCS gene family in plants: the history of gene duplication, sub/neofunctionalization and redundancy. Mol Genet Genomics 291, 739–752 (2016).

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  • KCS genes
  • Evolution
  • Expansion
  • Functional divergence
  • Redundancy