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The First Flax Genome Assembly

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Genetics and Genomics of Linum

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 23))

Abstract

Flax has been used as a crop for millennia, but its molecular resources have developed more slowly than other crop or model systems. However, the advent of next-generation sequencing provided a cost-effective methodology for developing whole genome assemblies from a range of plants. Flax was the first plant genome assembly to show that whole genome shotgun and next-generation sequencing (NGS) technologies could be used together, exclusive of any other information, and that this combination alone was sufficient to produce assemblies with high contiguity. The resulting flax genome assembly, which is now the reference genome for this species, consisted of 318 Mbp (in scaffolds), which contained approximately 85% of the actual genome, as measured by flow cytometry. The assembly was validated using independent genomic sequence information including expressed sequence tags, bacterial artificial chromosomes, and fosmids. This reference genome has contributed to the development of many other molecular resources for flax and its wild relatives.

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References

  • Burnett PGG, Olivia CM, Okinyo-Owiti DP, Reaney MJT (2016) Orbitide composition of the Flax Core Collection (FCC). J Agric Food Chem 64(25):5197–5206

    Article  CAS  Google Scholar 

  • Chantreau M, Chabbert B, Billiard S, Hawkins S, Neutelings G (2015) Functional analyses of cellulose synthase genes in flax (Linum usitatissimum) by virus-induced gene silencing. Plant Biotechnol J 13(9):1312–1324

    Article  CAS  Google Scholar 

  • Chen YM, Schneeberger RG, Cullis CA (2005) A site-specific insertion sequence in flax genotrophs induced by environment. New Phytol 167(1):171–180

    Article  CAS  Google Scholar 

  • Cullis C (1973) DNA differences between flax genotrophs. Nature 243:515–516

    Article  CAS  Google Scholar 

  • Cullis CA (1981) DNA-sequence organization in the flax genome. Biochim Biophys Acta 652(1):1–15

    Article  CAS  Google Scholar 

  • Darwin C (1863) On the existence of two forms, and on their reciprocal sexual relations, in several species of the genus Linum. J Linn Soci Bot 7:69–83

    Google Scholar 

  • Esau K (1942) Vascular differentiation in the vegetative shoot of Linum. I. The procambium. Am J Bot 29(9):738–747

    Article  Google Scholar 

  • Faruque K, Begam R, Deyholos MK (2015) The Amaranthin-Like Lectin (LuALL) genes of flax: a unique gene family with members inducible by Defence hormones. Plant Mol Biol Report 33(3):731–741

    Article  CAS  Google Scholar 

  • Flor HH (1955) Host-parasite interaction in flax rust—its genetics and other implications. Phytopathology 45:680–685

    Google Scholar 

  • Gavazzi F, Pigna G, Braglia L, Giani S, Breviario D, Morello L (2017) Evolutionary characterization and transcript profiling of beta-tubulin genes in flax (Linum usitatissimum L.) during plant development. BMC Plant Biol 17:237

    Article  Google Scholar 

  • Goff SA, Schnable JC, Feldmann KA (2014) The evolution of plant gene and genome sequencing. Advances in Botanical Research 69:47–90

    Google Scholar 

  • Gonzalez LG, Deyholos MK (2012) Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome. BMC Genomics 13:644

    Article  Google Scholar 

  • Initiative AG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen ZT, Tanzer A, Saunders ACE, Chi JX, Yang FT, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318(5849):420–426

    Article  CAS  Google Scholar 

  • Lane TS, Rempe CS, Davitt J, Staton ME, Peng YH, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, Rothfels CJ, Stevenson D, Graham SW, Yu J, Liu T, Pires JC, Edger PP, Zhang Y, Xie YL, Zhu Y, Carpenter E, Wong GKS, Stewart CN (2016) Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnol 16:47

    Article  Google Scholar 

  • Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967

    Article  CAS  Google Scholar 

  • Li RQ, Fan W, Tian G, Zhu HM, He L, Cai J, Huang QF, Cai QL, Li B, Bai YQ, Zhang ZH, Zhang YP, Wang W, Li J, Wei FW, Li H, Jian M, Li JW, Zhang ZL, Nielsen R, Li DW, Gu WJ, Yang ZT, Xuan ZL, Ryder OA, Leung FCC, Zhou Y, Cao JJ, Sun X, Fu YG, Fang XD, Guo XS, Wang B, Hou R, Shen FJ, Mu B, Ni PX, Lin RM, Qian WB, Wang GD, Yu C, Nie WH, Wang JH, Wu ZG, Liang HQ, Min JM, Wu Q, Cheng SF, Ruan J, Wang MW, Shi ZB, Wen M, Liu BH, Ren XL, Zheng HS, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie XY, Lu ZH, Zheng HC, Li YR, Steiner CC, Lam TTY, Lin SY, Zhang QH, Li GQ, Tian J, Gong TM, Liu HD, Zhang DJ, Fang L, Ye C, Zhang JB, Hu WB, Xu AL, Ren YY, Zhang GJ, Bruford MW, Li QB, Ma LJ, Guo YR, An N, Hu YJ, Zheng Y, Shi YY, Li ZQ, Liu Q, Chen YL, Zhao J, Qu N, Zhao SC, Tian F, Wang XL, Wang HY, Xu LZ, Liu X, Vinar T, Wang YJ, Lam TW, Yiu SM, Liu SP, Zhang HM, Li DS, Huang Y, Wang X, Yang GH, Jiang Z, Wang JY, Qin N, Li L, Li JX, Bolund L, Kristiansen K, Wong GKS, Olson M, Zhang XQ, Li SG, Yang HM, Wang J, Wang J (2010) The sequence and de novo assembly of the giant panda genome. Nature 463(7279):311–317

    Article  CAS  Google Scholar 

  • McDill J, Repplinger M, Simpson BB, Kadereit JW (2009) The phylogeny of Linum and Linaceae subfamily Linoideae, with implications for their systematics, biogeography, and evolution of heterostyly. Syst Bot 34(2):386–405

    Article  Google Scholar 

  • McDill JR, Simpson BB (2011) Molecular phylogenetics of Linaceae with complete generic sampling and data from two plastid genes. Bot J Linn Soc 165(1):64–83

    Article  Google Scholar 

  • Mokshina N, Gorshkova T, Deyholos MK (2014) Chitinase-Like (CTL) and Cellulose Synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) Bast fibers. PLoS One 9(6):e97949

    Article  Google Scholar 

  • Oplinger ES, Oelke EA, Doll JD, Bundy LG, Schuler RT (1989) Flax. Alternative field crops manual. University of Minnesota, St. Paul, MN

    Google Scholar 

  • Pinzón-Latorre D, Deyholos MK (2013) Characterization and expression of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum). BMC Genomics 14:742

    Article  Google Scholar 

  • Preisner M, Wojtasik W, Kostyn K, Boba A, Czuj T, Szopa J, Kulma A (2018) The cinnamyl alcohol dehydrogenase family in flax: differentiation during plant growth and under stress conditions. J Plant Physiol 221:132–143

    Article  CAS  Google Scholar 

  • Ragupathy R, Rathinavelu R, Cloutier S (2011) Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. BMC Genomics 12(1):217

    Article  CAS  Google Scholar 

  • Richly E, Leister D (2004) NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. Mol Biol Evol 21(10):1972–1980

    Article  CAS  Google Scholar 

  • Rowland GG, Hormis YA, Rashid KY (2002) CDC Bethune flax. Can J Plant Sci 82(1):101–102

    Article  Google Scholar 

  • Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596–1604

    Article  CAS  Google Scholar 

  • Ushijima K, Nakano R, Bando M, Shigezane Y, Ikeda K, Namba Y, Kume S, Kitabata T, Mori H, Kubo Y (2012) Isolation of the floral morph-related genes in heterostylous flax (Linum grandiflorum): the genetic polymorphism and the transcriptional and post-transcriptional regulations of the S locus. Plant J 69(2):317–331

    Article  CAS  Google Scholar 

  • Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GKS, Wang J, Deyholos MK (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72(3):461–473

    Article  Google Scholar 

  • Waring M, Britten RJ (1966) Nucleotide sequence repetition – a rapidly REASSOCIATING fraction of mouse DNA. Science 154(3750):791

    Article  CAS  Google Scholar 

  • Yurkevich OY, Kirov IV, Bolsheva NL, Rachinskaya OA, Grushetskaya ZE, Zoschuk SA, Samatadze TE, Bogdanova MV, Lemesh VA, Amosova AV, Muravenko OV (2017) Integration of physical, genetic, and cytogenetic mapping data for Cellulose Synthase (CesA) genes in flax (Linum usitatissimum L.). Front Plant Sci 8

    Google Scholar 

  • Zohary D, Hopf M (2000) Domestication of plants in the Old World: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley. Oxford University Press, Oxford, UK

    Google Scholar 

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Authors and Affiliations

  1. University of British Columbia, Okanagan, Kelowna, BC, Canada

    Michael K. Deyholos

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  1. Michael K. Deyholos
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Correspondence to Michael K. Deyholos .

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Editors and Affiliations

  1. Department of Biology, Case Western Reserve University, Cleveland, OH, USA

    Christopher A. Cullis

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Deyholos, M.K. (2019). The First Flax Genome Assembly. In: Cullis, C. (eds) Genetics and Genomics of Linum. Plant Genetics and Genomics: Crops and Models, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-030-23964-0_4

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