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An Intact, But Dormant LTR Retrotransposon Defines a Moderately Sized Family in White Spruce (Picea glauca)

  • Britta Hamberger
  • Macaire Man Saint Yuen
  • Emmanuel Buschiazzo
  • Claire Cullis
  • Agnes Yuen
  • Carol Ritland
  • Jörg Bohlmann
  • Björn HambergerEmail author
Chapter
  • 126 Downloads
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Within seed plants, the genomes of the conifer lineage are extraordinarily large and complex. While the evolutionary mechanisms driving this expansion are poorly understood, increasing evidence implicates retrotransposon activity as the driving force. We have isolated in targeted fashion and sequenced two independent white spruce genomic BAC clones for CYP701A24, involved in the biosynthesis of the phytohormone gibberellic acid. Sequence comparison showed little similarity between the two clones, one carrying the bona fide target CYP701A24 and the other an intronless fragment of a CYP701A24 pseudogene. In proximity of both CYP701A24 loci, we detected several signatures of the long terminal repeat (LTR) retrotransposon class. Sequence characterization identified one outstanding Ty3-gypsy class element, which was termed Picnicker1 for its size and degree of sequence conservation in the LTR. Representation of its homologous sequence in genomic amplicons and within the white spruce draft genome revealed that Picnicker1 is the founding member of a moderately sized family. Dating of the insertion event with the synonymous substitution rate applied to the nucleotide polymorphisms of the LTR suggested an age postdating major speciation in spruce. Independent support for an evolutionary recent incident was provided by an investigation of the genomic locus in a range of spruce species with increasing relatedness to white spruce, and in white spruce for a range of geographical origins. Transcript evidence revealed that related members of the family, but not Picnicker1 still flourish as part of the dynamic content in modern spruce genomes.

Keywords

Gene duplication mechanism General metabolism BAC sequencing Picnicker Dating LTR-retrotransposon Young evolutionary marker 

Notes

Acknowledgements

We are grateful to Armand Séguin of the Canadian Forest Service, Laurentian Forestry Centre, Quebec City, Quebec, Canada) for shared material of the white spruce clonal line PG653 and Barry Jaquish of the B.C. Ministry of Forests and Range and for tissue of Engelmann spruce. Bj.H. acknowledges current support, which permitted finishing this manuscript, by the U.S. Department of Energy-Great Lakes Bioenergy Research Center Cooperative Agreement DE-FC02-07ER64494 and DE-SC0018409, the Michigan State University Strategic Partnership Grant program ‘Plant-inspired Chemical Diversity’, recruitment funding from the Department of Molecular Biology and Biochemistry, Michigan State University and support from Michigan State University AgBioResearch (MICL02454). Bj.H. is in part supported by the National Science Foundation under Grant Number 1737898. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Supplementary material

476904_1_En_4_MOESM1_ESM.pdf (230 kb)
Supplementary material 1 (PDF 229 kb)

References

  1. Anderson LL, Hu FS, Nelson DM et al (2006) Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proc Natl Acad Sci 103:12447 LP–12450Google Scholar
  2. Bennett M, Leitch I (2012) Angiosperm DNA C-values database (release 8.0, Dec. 2012). http://www.kew.org/cvalues/
  3. Birol I, Raymond A, Jackman SD et al (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29:1492–1497PubMedPubMedCentralGoogle Scholar
  4. Bouillé M, Bousquet J (2005) Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees. Am J Bot 92:63–73PubMedGoogle Scholar
  5. Buschiazzo E, Ritland C, Bohlmann J, Ritland K (2012) Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol 12:8PubMedPubMedCentralGoogle Scholar
  6. Chavanne F, Zhang D-X, Liaud M-F, Cerff R (1998) Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species. Plant Mol Biol 37:363–375PubMedGoogle Scholar
  7. Chen J, Källman T, Gyllenstrand N, Lascoux M (2009) New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict. Heredity (Edinb) 104:3Google Scholar
  8. De La Torre A, Birol I, Bousquet J et al (2014a) Insights into conifer giga-genomes. Plant Physiol 166:1724–1732Google Scholar
  9. De La Torre AR, Roberts DR, Aitken SN (2014b) Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow. Mol Ecol 23:2046–2059Google Scholar
  10. de Lafontaine G, Turgeon J, Payette S (2010) Phylogeography of white spruce (Picea glauca) in eastern North America reveals contrasting ecological trajectories. J Biogeogr 37:741–751Google Scholar
  11. Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12:1075–1079PubMedPubMedCentralGoogle Scholar
  12. Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 18:1176–1188PubMedGoogle Scholar
  13. Gao X, Havecker ER, Baranov PV et al (2003) Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA 9:1422–1430PubMedPubMedCentralGoogle Scholar
  14. Hamberger B, Bohlmann J (2006) Cytochrome P450 mono-oxygenases in conifer genomes: discovery of members of the terpenoid oxygenase superfamily in spruce and pine. Biochem Soc Trans 34:1209 LP–1214Google Scholar
  15. Hamberger B, Hall D, Yuen M et al (2009) Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome. BMC Plant Biol 9Google Scholar
  16. Hamberger B, Ohnishi T, Hamberger B et al (2011) Evolution of diterpene metabolism: sitka spruce CYP720B4 catalyzes multiple oxidations in resin acid biosynthesis of conifer defense against insects. Plant Physiol 157:1677–1695PubMedPubMedCentralGoogle Scholar
  17. Jun J, Ryvkin P, Hemphill E, Nelson C (2009) Duplication mechanism and disruptions in flanking regions determine the fate of mammalian gene duplicates. J Comput Biol 16:1253–1266PubMedGoogle Scholar
  18. Kalendar R, Schulman AH (2007) IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protoc 1:2478Google Scholar
  19. Kamm A, Doudrick RL, Heslop-Harrison JS, Schmidt T (1996) The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc Natl Acad Sci 93:2708 LP–2713Google Scholar
  20. Keeling CI, Dullat HK, Yuen M et al (2010) Identification and functional characterization of monofunctional ent-copalyl diphosphate and ent-kaurene synthases in white spruce reveal different patterns for diterpene synthase evolution for primary and seconda. Plant Physiol 152:1197 LP–1208Google Scholar
  21. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483–1498PubMedGoogle Scholar
  22. Koduri PKH, Gordon GS, Barker EI et al (2010) Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens. Plant Mol Biol 72:247–263PubMedGoogle Scholar
  23. Kossack DS, Kinlaw CS (1999) IFG, a gypsy-like retrotransposon in Pinus (Pinaceae), has an extensive history in pines. Plant Mol Biol 39:417–426PubMedGoogle Scholar
  24. Kovach A, Wegrzyn JL, Parra G et al (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11:420PubMedPubMedCentralGoogle Scholar
  25. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532PubMedGoogle Scholar
  26. L’Homme Y, Seguin A, Tremblay F (2001) Different classes of retrotransposons in coniferous spruce speciesGoogle Scholar
  27. LePage B (2001) New species of Picea A. Dietrich (Pinaceae) from the middle Eocene of Axel Heiberg Island, Arctic Canada. Bot J Linn Soc 135:137–167Google Scholar
  28. Lisch D, Bennetzen JL (2011) Transposable element origins of epigenetic gene regulation. Curr Opin Plant Biol 14:156–161PubMedGoogle Scholar
  29. Lisch D, Slotkin RK (2011) Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts (Jeon KWBT-IR of C and MB (ed)). Academic Press, pp 119–152Google Scholar
  30. Lockwood JD, Aleksić JM, Zou J et al (2013) A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences. Mol Phylogenet Evol 69:717–727PubMedGoogle Scholar
  31. Magbanua Z V, Ozkan S, Bartlett BD, et al (2011) Adventures in the Enormous: A 1.8 Million Clone BAC Library for the 21.7 Gb Genome of Loblolly Pine. PLoS One 6:e16214Google Scholar
  32. Martínez-Izquierdo JA, García-Martínez J, Vicient CM (1997) What makes Grande1 retrotransposon different? Genetica 100:15–28PubMedGoogle Scholar
  33. Moisy C, Garrison KE, Meredith CP, Pelsy F (2008) Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome. BMC Genomics 9:469PubMedPubMedCentralGoogle Scholar
  34. Morse AM, Peterson DG, Islam-Faridi MN et al (2009) Evolution of genome size and complexity in Pinus. PLoS ONE 4:e4332PubMedPubMedCentralGoogle Scholar
  35. Neale DB, Wegrzyn JL, Stevens KA et al (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15:R59PubMedPubMedCentralGoogle Scholar
  36. Nystedt B, Street NR, Wetterbom A et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579PubMedGoogle Scholar
  37. Piegu B, Guyot R, Picault N et al (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269PubMedPubMedCentralGoogle Scholar
  38. Ragupathy R, Banks T, Cloutier S (2010) Molecular characterization of the Sasanda LTR copia retrotransposon family uncovers their recent amplification in Triticum aestivum (L.) genome. Mol Genet Genomics 283:255–271PubMedGoogle Scholar
  39. Rake AV, Miksche JP, Hall RB, Hansen KM (1980) DNA reassociation kinetics of four conifers. Can J Genet Cytol 22:69–79Google Scholar
  40. Ran J-H, Wei X-X, Wang X-Q (2006) Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes. Mol Phylogenet Evol 41:405–419PubMedGoogle Scholar
  41. Rocheta M, Cordeiro J, Oliveira M, Miguel C (2007) PpRT1: the first complete gypsy-like retrotransposon isolated in Pinus pinaster. Planta 225:551–562PubMedGoogle Scholar
  42. Rungis D, Bérubé Y, Zhang J et al (2004) Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor Appl Genet 109:1283–1294PubMedGoogle Scholar
  43. SanMiguel P, Gaut BS, Tikhonov A et al (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43PubMedGoogle Scholar
  44. Shedlock AM, Takahashi K, Okada N (2004) SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol 19:545–553PubMedGoogle Scholar
  45. Smit AFA, Hubley R, Green P (2017) 1996–2010. RepeatMasker Open-3.0Google Scholar
  46. Stival Sena J, Giguère I, Boyle B et al (2014) Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biol 14:95PubMedPubMedCentralGoogle Scholar
  47. Stuart-Rogers C, Flavell AJ (2001) The evolution of Ty1-copia group retrotransposons in gymnosperms. Mol Biol Evol 18:155–163PubMedGoogle Scholar
  48. Syed NH, Flavell AJ (2007) Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nat Protoc 1:2746Google Scholar
  49. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedGoogle Scholar
  50. Thibaud-Nissen F, Ouyang S, Buell CR (2009) Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics 10:317PubMedPubMedCentralGoogle Scholar
  51. Warren RL, Keeling CI, Saint Yuen MM et al (2015) Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. Plant J 83:189–212PubMedGoogle Scholar
  52. Wicker T, Sabot F, Hua-Van A et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973PubMedGoogle Scholar
  53. Wright DA, Voytas DF (1998) Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3-gypsy retrotransposons that encode envelope-like proteins. Genetics 149:703 LP–715Google Scholar
  54. Xu Z, Wang H (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucl Acids Res 35:W265–W268PubMedGoogle Scholar
  55. Zuccolo A, Scofield DG, De Paoli E, Morgante M (2015) The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200MY of evolution. Gene 568:89–99PubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Britta Hamberger
    • 1
    • 3
    • 4
  • Macaire Man Saint Yuen
    • 1
  • Emmanuel Buschiazzo
    • 2
    • 5
  • Claire Cullis
    • 2
  • Agnes Yuen
    • 2
  • Carol Ritland
    • 2
  • Jörg Bohlmann
    • 1
    • 2
  • Björn Hamberger
    • 1
    • 3
    • 4
    Email author
  1. 1.Michael Smith LaboratoriesThe University of British ColumbiaVancouverCanada
  2. 2.Department of Forest SciencesThe University of British ColumbiaVancouverCanada
  3. 3.Department of Biochemistry & Molecular BiologyMichigan State UniversityEast LansingUSA
  4. 4.Molecular Plant Sciences BuildingEast LansingUSA
  5. 5.School of Natural SciencesUniversity of CaliforniaMercedUSA

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