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

Springer Science and Business Media LLC - Tập 10 Số 1 - 2010
Carolyn Hutcheon1, Renata Fava Ditt1, Mark A. Beilstein2, Luca Comai3, Jesara L. Schroeder1, Elianna Goldstein3, Christine K. Shewmaker4, Thu Trang Nguyen1, Jay De Rocher1, Jack Kiser5
1Targeted Growth, Inc., 2815 Eastlake Ave E Suite 300, Seattle, WA, 98102, USA
2Dept. of Biochemistry/Biophysics, Texas A&M University, TAMU 2128 College Station, TX, 77843, USA
3Plant Biology and Genome Center, 451 Health Sciences Drive, University of California Davis, Davis, CA, 95616, USA
4BluGoose Consulting, Woodland, CA, 95776, USA
5Sustainable Oils, LLC, 3208 Curlew St., Davis, CA, 95616, USA

Tóm tắt

Abstract Background Camelina 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. Results In 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. Conclusions There 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.

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Tài liệu tham khảo

Putnam D, Budin J, Field L, Breene W: Camelina: a promising low-input oilseed. New crops. Edited by: Janick J, Simon JE. New York: Wiley, 1993:314-322.

Gehringer A, Friedt W, Luhs W, Snowdon RJ: Genetic mapping of agronomic traits in false flax (Camelina sativa subsp. sativa). Genome. 2006, 49: 1555-1563. 10.1139/G06-117.

Beilstein MA, Al-Shehbaz IA, Kellogg EA: Brassicaceae phylogeny and trichome evolution. Am J Bot. 2006, 93: 607-619. 10.3732/ajb.93.4.607.

Beilstein MA, Al-Shehbaz IA, Mathews S, Kellogg EA: Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited. Am J Bot. 2008, 95: 1307-1327. 10.3732/ajb.0800065.

Budin J, Breene W, Putnam D: Some compositional properties of camelina (camelina sativa L. Crantz) seeds and oils. Journal of the American Oil Chemists' Society. 1995, 72: 309-315. 10.1007/BF02541088.

Frohlich A, Rice B: Evaluation of Camelina sativa oil as a feedstock for biodiesel production. Industrial Crops and Products. 2005, 21: 25-31. 10.1016/j.indcrop.2003.12.004.

Bernardo A, Howard-Hildige R, O'Connell A, Nichol R, Ryan J, Rice B, Roche E, Leahy JJ: Camelina oil as a fuel for diesel transport engines. Industrial Crops and Products. 2003, 17: 191-197. 10.1016/S0926-6690(02)00098-5.

Akeroyd J: Camelina in Flora Europaea. Cambridge, UK: Cambridge University Press;, 2 1993.

Mirek Z: Genus Camelina in Poland - Taxonomy, Distribution and Habitats. Fragmenta Floristica et Geobotanica. 1981, 27: 445-503.

Brooks RE: Chromosome number reports LXXXVII. Taxon. 1985, 34: 346-351.

Baksay L: The chromosome numbers and cytotaxonomical relations of some European plant species. Ann Hist-Nat Mus Natl Hung. 1957, 169-174.

Maassoumi A: Cruciferes de la flore d'Iran: etude caryosystematique. Strasbourg, France; 1980.

Francis A, Warwick S: The Biology of Canadian Weeds. 142. Camelina alyssum (Mill.) Thell.; C. microcarpa Andrz. ex DC.; C. sativa (L.) Crantz. Canadian Journal of Plant Science. 2009, 89: 791-810. 10.4141/CJPS08185.

Tedin O: Vererbung, Variation und Systematik in der Gattung Camelina. Hereditas. 1925, 6: 19-386.

Flannery ML, Mitchell FJ, Coyne S, Kavanagh TA, Burke JI, Salamin N, Dowding P, Hodkinson TR: Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs. Theor Appl Genet. 2006, 113: 1221-1231. 10.1007/s00122-006-0377-0.

Vollmann J, Grausgruber H, Stift G, Dryzhyruk V, Lelley T: Genetic diversity in camelina germplasm as revealed by seed quality characteristics and RAPD polymorphism. Plant Breeding. 2005, 124: 446-453. 10.1111/j.1439-0523.2005.01134.x.

Martynov VV, Tsvetkov IL, Khavkin EE: Orthologs of arabidopsis CLAVATA 1 gene in cultivated Brassicaceae plants. Ontogenez. 2004, 35: 41-46.

Zubr J, Matthaus B: Effects of growth conditions on fatty acids and tocopherols in Camelina sativa oil. Industrial Crops and Products. 2002, 15: 155-162. 10.1016/S0926-6690(01)00106-6.

Durrett TP, Benning C, Ohlrogge J: Plant triacylglycerols as feedstocks for the production of biofuels. Plant J. 2008, 54: 593-607. 10.1111/j.1365-313X.2008.03442.x.

Okuley J, Lightner J, Feldmann K, Yadav N, Lark E, Browse J: Arabidopsis FAD2 gene encodes the enzyme that is essential for polyunsaturated lipid synthesis. Plant Cell. 1994, 6: 147-158. 10.1105/tpc.6.1.147.

Miquel M, Browse J: Arabidopsis mutants deficient in polyunsaturated fatty acid synthesis. Biochemical and genetic characterization of a plant oleoyl-phosphatidylcholine desaturase. J Biol Chem. 1992, 267: 1502-1509.

Hongtrakul V, Slabaugh MB, Knapp SJ: A Seed Specific {Delta}-12 Oleate Desaturase Gene Is Duplicated, Rearranged, and Weakly Expressed in High Oleic Acid Sunflower Lines. Crop Sci. 1998, 38: 1245-1249. 10.2135/cropsci1998.0011183X003800050022x.

Patel M, Jung S, Moore K, Powell G, Ainsworth C, Abbott A: High-oleate peanut mutants result from a MITE insertion into the FAD2 gene. Theor Appl Genet. 2004, 108: 1492-1502. 10.1007/s00122-004-1590-3.

Hu X, Sullivan-Gilbert M, Gupta M, Thompson SA: Mapping of the loci controlling oleic and linolenic acid contents and development of fad2 and fad3 allele-specific markers in canola (Brassica napus L.). Theor Appl Genet. 2006, 113: 497-507. 10.1007/s00122-006-0315-1.

Kunst L, Taylor D, Underhill E: Fatty acid elongation in developing seeds of Arabidopsis thaliana. Plant Physiol Biochem. 1992, 30: 425-434.

James DW, Lim E, Keller J, Plooy I, Ralston E, Dooner HK: Directed Tagging of the Arabidopsis FATTY ACID ELONGATION1 (FAE1) Gene with the Maize Transposon Activator. Plant Cell. 1995, 7: 309-319. 10.1105/tpc.7.3.309.

Wang N, Wang Y, Tian F, King GJ, Zhang C, Long Y, Shi L, Meng J: A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol. 2008, 180: 751-765. 10.1111/j.1469-8137.2008.02619.x.

Wu G, Wu Y, Xiao L, Li X, Lu C: Zero erucic acid trait of rapeseed (Brassica napus L.) results from a deletion of four base pairs in the fatty acid elongase 1 gene. Theor Appl Genet. 2008, 116: 491-499. 10.1007/s00122-007-0685-z.

Katavic V, Mietkiewska E, Barton DL, Giblin EM, Reed DW, Taylor DC: Restoring enzyme activity in nonfunctional low erucic acid Brassica napus fatty acid elongase 1 by a single amino acid substitution. Eur J Biochem. 2002, 269: 5625-5631. 10.1046/j.1432-1033.2002.03270.x.

Comai L: The advantages and disadvantages of being polyploid. Nat Rev Genet. 2005, 6: 836-846. 10.1038/nrg1711.

Sybenga J: Chromosome pairing affinity and quadrivalent formation in polyploids: do segmental allopolyploids exist?. Genome. 1996, 39: 1176-1184. 10.1139/g96-148.

Blanc G, Wolfe KH: Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell. 2004, 16: 1667-1678. 10.1105/tpc.021345.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al: Genome sequence of the palaeopolyploid soybean. Nature. 2010, 463: 178-183. 10.1038/nature08670.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al: The B73 maize genome: complexity, diversity, and dynamics. Science. 2009, 326: 1112-1115. 10.1126/science.1178534.

Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW: Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol. 2010, 10: 61-10.1186/1471-2148-10-61.

The Arabidopsis Information Resource. [http://www.arabidopsis.org]

Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'Bleness M, Roe BA, Nelson RT, Scheffler BE, et al: Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics. 2007, 8: 330-10.1186/1471-2164-8-330.

Scheffler JA, Sharpe AG, Schmidt H, Sperling P, Parkin IAP, Lühs W, Lydiate DJ, Heinz E: Desaturase multigene families of Brassica napus arose through genome duplication. Theor Appl Genet. 1997, 94: 583-591. 10.1007/s001220050454.

Hernandez ML, Mancha M, Martinez-Rivas JM: Molecular cloning and characterization of genes encoding two microsomal oleate desaturases (FAD2) from olive. Phytochemistry. 2005, 66: 1417-1426. 10.1016/j.phytochem.2005.04.004.

Mikkilineni V, Rocheford TR: Sequence variation and genomic organization of fatty acid desaturase-2 (fad2) and fatty acid desaturase-6 (fad6) cDNAs in maize. Theor Appl Genet. 2003, 106: 1326-1332.

Martínez-Rivas JM, Sperling P, Lühs W, Heinz E: Spatial and temporal regulation of three different microsomal oleate desaturase genes (FAD2) from normal-type and high-oleic varieties of sunflower (Helianthus annuus L.). Molecular Breeding. 2001, 8: 159-168. 10.1023/A:1013324329322.

Frohlich MW, Estabrook GF: Wilkinson support calculated with exact probabilities: an example using Floricaula/LEAFY amino acid sequences that compares three hypotheses involving gene gain/loss in seed plants. Mol Biol Evol. 2000, 17: 1914-1925.

Kim MJ, Kim H, Shin JS, Chung CH, Ohlrogge JB, Suh MC: 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 Genomics. 2006, 276: 351-368. 10.1007/s00438-006-0148-2.

Tocher DRLM, Hodgson PA: Recent advances in the biochemistry and molecular biology of fatty acyl desaturases. Progress in Lipid Research. 1998, 37: 73-117. 10.1016/S0163-7827(98)00005-8.

McCartney AW, Dyer JM, Dhanoa PK, Kim PK, Andrews DW, McNew JA, Mullen RT: Membrane-bound fatty acid desaturases are inserted co-translationally into the ER and contain different ER retrieval motifs at their carboxy termini. Plant J. 2004, 37: 156-173. 10.1111/j.1365-313X.2004.01949.x.

Belo A, Zheng P, Luck S, Shen B, Meyer DJ, Li B, Tingey S, Rafalski A: Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics. 2008, 279: 1-10. 10.1007/s00438-007-0289-y.

Cahoon EB, Marillia EF, Stecca KL, Hall SE, Taylor DC, Kinney AJ: Production of fatty acid components of meadowfoam oil in somatic soybean embryos. Plant Physiol. 2000, 124: 243-251. 10.1104/pp.124.1.243.

Mietkiewska E, Giblin EM, Wang S, Barton DL, Dirpaul J, Brost JM, Katavic V, Taylor DC: Seed-specific heterologous expression of a nasturtium FAE gene in Arabidopsis results in a dramatic increase in the proportion of erucic acid. Plant Physiol. 2004, 136: 2665-2675. 10.1104/pp.104.046839.

Ghanevati M, Jaworski JG: Engineering and mechanistic studies of the Arabidopsis FAE1 beta-ketoacyl-CoA synthase, FAE1 KCS. Eur J Biochem. 2002, 269: 3531-3539. 10.1046/j.1432-1033.2002.03039.x.

Ghanevati M, Jaworski JG: Active-site residues of a plant membrane-bound fatty acid elongase beta-ketoacyl-CoA synthase, FAE1 KCS. Biochim Biophys Acta. 2001, 1530: 77-85.

Ruuska SA, Girke T, Benning C, Ohlrogge JB: Contrapuntal networks of gene expression during Arabidopsis seed filling. Plant Cell. 2002, 14: 1191-1206. 10.1105/tpc.000877.

Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B: Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell. 2000, 12: 1551-1568. 10.1105/tpc.12.9.1551.

Kashkush K, Feldman M, Levy AA: Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics. 2002, 160: 1651-1659.

He P, Friebe BR, Gill BS, Zhou JM: Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol. 2003, 52: 401-414. 10.1023/A:1023965400532.

Adams KL, Percifield R, Wendel JF: Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics. 2004, 168: 2217-2226. 10.1534/genetics.104.033522.

Park C, Correll D, Oeth P: Measuring Allele-Specific Expression Using MassARRAY. 2004, Doc No.8876-005 R01

Nucleic Acid Dot Plots. [http://www.vivo.colostate.edu/molkit/dnadot/index.html]

Posada D, Crandall K: Modeltest: testing the model of DNA substitution. Bioinformatics. 1998, 14: 817-818. 10.1093/bioinformatics/14.9.817.

Swofford D: PAUP* 4.0 beta 5: Phylogenetic Analysis Using Parsimony and Other Methods. Sinauer; 2001.

Gugel RK, Falk KC: Agronomic and seed quality evaluation of Camelina sativa in western Canada. Canadian journal of plant science. 2006, 86: 1047-1058.

Zubr J: Oil-seed crop: Camelina sativa. Industrial Crops and Products. 1997, 6: 113-119. 10.1016/S0926-6690(96)00203-8.

Moon H, Smith MA, Kunst L: A Condensing Enzyme from the Seeds of Lesquerella fendleri That Specifically Elongates Hydroxy Fatty Acids. Plant Physiol. 2001, 127: 1635-1643. 10.1104/pp.010544.

TIGR Rice Database. [http://rice.tigr.org/]

Phytozome. [http://www.phytozome.net/index.php]

Maize Genome Browser. [http://maizesequence.org/index.html]

Lu C, Kang J: Generation of transgenic plants of a potential oilseed crop Camelina sativa by Agrobacterium-mediated transformation. Plant Cell Reports. 2008, 27: 273-278. 10.1007/s00299-007-0454-0.

Salmon A, Ainouche ML, Wendel JF: Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology. 2005, 14: 1163-1175. 10.1111/j.1365-294X.2005.02488.x.

Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen A-C, Elven R: Polyploidy in arctic plants. Biological Journal of the Linnean Society. 2004, 82: 521-536. 10.1111/j.1095-8312.2004.00337.x.

USDA Germplasm Resources Information Network. [http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en]

Hegarty MJ, Hiscock SJ: Genomic Clues to the Evolutionary Success of Polyploid Plants. Current Biology. 2008, 18: R435-R444. 10.1016/j.cub.2008.03.043.

Dubcovsky J, Dvorak J: Genome plasticity a key factor in the success of polyploid wheat under domestication. Science. 2007, 316: 1862-1866. 10.1126/science.1143986.

Gill BS, Friebe B: Plant cytogenetics at the dawn of the 21st century. Current Opinion in Plant Biology. 1998, 1: 109-115. 10.1016/S1369-5266(98)80011-3.

Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D: A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol. 2005, 23: 75-81. 10.1038/nbt1043.

Cooper J, Till B, Laport R, Darlow M, Kleffner J, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, et al: TILLING to detect induced mutations in soybean. BMC Plant Biology. 2008, 8: 9-10.1186/1471-2229-8-9.

Swaminathan MS, Rao MV: Frequency of Mutations Induced by Radiations in Hexaploid Species of Triticum. Science. 1960, 132: 1842-10.1126/science.132.3442.1842.

Stadler LJ: Chromosome Number and the Mutation Rate in Avena and Triticum. Proc Natl Acad Sci USA. 1929, 15: 876-881. 10.1073/pnas.15.12.876.

Muramatsu M: Dosage Effect of the Spelta Gene q of Hexaploid Wheat. Genetics. 1963, 48: 469-482.

Li W, Huang L, Gill BS: Recurrent Deletions of Puroindoline Genes at the Grain Hardness Locus in Four Independent Lineages of Polyploid Wheat1. Plant Physiol. 2008, 146: 200-212. 10.1104/pp.107.108852.

Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW: Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA. 1984, 81: 8014-8018. 10.1073/pnas.81.24.8014.

Maniatis T, Sambrook J, Fritsch EF: Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1982.

Boxshade. [http://www.ch.embnet.org/]

Tai HH, Pelletier C, Beardmore T: Total RNA isolation from Picea mariana dry seed. Plant Molecular Biolgy Reporter. 2004, 22: 93a-93e. 10.1007/BF02773357.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.

Maddison W, Maddison DR: MacClade: analysis of phylogeny and character evolution. 2004, Sinauer, Version 4.05

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