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Geographical gradients in the genome size variation of wild coffee trees (Coffea) native to Africa and Indian Ocean islands

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Abstract

The genus Coffea, mainly native to Africa and to the Indian Ocean islands (Mascarocoffea), accounts for 124 species. Genome size data are available for 23 African species. The aim of this study was to assess the genome size of 44 Mascarocoffea species and to investigate possible association with species geographic distribution, stomata traits, and species relationships. 2 C values were measured using flow cytometry. A lyophilization procedure for leaves was tested. The 2 C nuclear DNA content of Mascarocoffea species ranged from 0.96 to 1.41 pg. Coffea mauritiana and Coffea humblotiana have the smallest genomes and Coffea millotii has the largest. Mean 2 C DNA for Mascarocoffea and Africa is 1.19 and 1.43 pg, respectively. The overall DNA values corresponded to two partially overlapped normal distributions: one harboring species from east Africa Mascarocoffea, the other harboring species from west/central Africa. Plotted on a geographical map according to the native origin of species, these values showed a gradient in Madagascar and Africa. Genome sizes increased following a north to southeast gradient in Madagascar and an east to west gradient in Africa. None, or only weak correlations were noted between genome size and stomata parameters. Genetically close species could be highly distinctive in their genome size while divergent species could be similarly sized. The non-random geographic distribution and habitat of species, and the absence of correlation between genome size and genetic relationships, suggest that during Coffea genome evolution, both DNA content increase and/or decrease occurred independently in Africa and in the Indian Ocean Islands.

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Abbreviations

FL:

Fresh leaves

GCL:

Guard cell length

HD:

Hierarchical clustering

HSD:

Honestly significant difference

LL:

Leaf length

LyL:

Lyophilized leaves

My:

Million years

PI:

Propidium Iodide

SD:

Stomata density

References

  • Anthony F, Clifford MN, Noirot M (1993) Biochemical diversity in the genus Coffea L, chlorogenic acids, caffeine and mozambioside contents. Genet Resour Crop Evol 40:61–70, 1993

    Article  Google Scholar 

  • Anthony F, Diniz LEC, Combes MC, Lashermes P (2010) Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar. Plant Syst Evol 285:51–64

    Article  Google Scholar 

  • Barre P, Noirot N, Louarn J, Duperray C, Hamon S (1996) Reliable flow cytometric estimation of nuclear DNA content in coffee trees. Cytometry 24:32–38

    Article  PubMed  CAS  Google Scholar 

  • Beaulieu JM, Leitch IJ, Knight CA (2007) Genome size evolution in relation to leaf strategy and metabolic rates revisited. Ann Bot 99:495–505

    Article  PubMed  CAS  Google Scholar 

  • Beaulieu JM, Leitch IJ, Patel S, Pendharkar A, Knight CA (2008) Genome size is a strong predictor of cell size and stomatal density in angiosperms. New Phytol 179:975–986

    Article  PubMed  Google Scholar 

  • Bennett MD (1987) Variation in genomic form in plants and its ecological implications. New Phytol 106:177–200

    Article  Google Scholar 

  • Bennett MD, Leitch IJ (2005) Plant genome size research: a field in focus. Ann Bot 95:1–6

    Article  PubMed  CAS  Google Scholar 

  • Bouharmont J (1959) Recherches sur les affinitĂ©s chromosomiques dans le genre Coffea. INEAC (Brussels), SĂ©rie Sci., 77, 94p

  • Bouharmont J (1963) Somatic chromosomes of some Coffea species. Euphytica 12:254–257

    Google Scholar 

  • Bretz F, Hothorn T, Westfall P (2010) Multiple comparisons using R. CRC Boca Raton R.2 .11. 1 http://cran r-project org

  • Brummitt RK with assistance from Pando F, Hollis S, Brummitt NA et al. (2001) Plant taxonomic database standards No. 2, 2nd edn. World geographical scheme for recording plant distributions, 2nd edn. Pittsburgh, PA: Hunt Institute for Botanical Documentation, Canege Mellon University

  • Caetano-Anollès G (2005) Evolution in genome size in grass. Crop Sci 45:1809–1816

    Article  Google Scholar 

  • Campa C, Doulbeau S, Dussert S, Hamon S, Noirot M (2005) Qualitative relationship between caffeine and chlorogenic acid contents among wild Coffea species. Food Chem 93:135–139

    Article  CAS  Google Scholar 

  • Charrier A (1978) La structure gĂ©nĂ©tique des cafĂ©iers spontanĂ©s de la rĂ©gion malgache (Mascarocoffea): leur relation avec les cafĂ©iers d'origine africaine (Eucoffea) PhD Thesis Edn ORSTOM Paris 224pp

  • Chevalier A (1947) Les cafĂ©iers du globe III : SystĂ©matique des cafĂ©iers et des faux cafĂ©iers Edn Paul Lechevalier Paris France 356pp

  • Coba de la Peña T, Brown SC (2001) Cytometry and fluorimetry. In: Hawes C, Satiat-JeunemaĂ®tre B (eds) Plant cell biology: a practical approach. Oxford University Press, Oxford, pp 85–106

    Google Scholar 

  • Cros J, Combes MC, Chabrillange N, Duperray C, Desangles AM, Hamon S (1995) Nuclear DNA content in the subgenus Coffea (Rubiaceae): inter and intra specific variation in African species. Can J Bot 73:14–20

    Article  Google Scholar 

  • Cros J, Combes MC, Trouslot P, Anthony F, Hamon S, Charrier A, Lashermes P (1998) Phylogenetic analysis of chloroplast DNA variation in Coffea L. Mol Phylogenet Evol 1:109–117

    Article  Google Scholar 

  • Davis AP, Govaerts R, Bridson DM, Stoffelen P (2006) An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Bot J Linn Soc 152:465–512

    Article  Google Scholar 

  • Davis AP, Tosh J, Ruch N, Fay M (2011) Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size, morphology, distribution and evolutionary history of Coffea. Bot J Linn Soc 167:357–377

    Article  Google Scholar 

  • DoleĹľel J, Bartoš J (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Ann Bot 95:99–110

    Article  PubMed  Google Scholar 

  • Dušková E, Kolar F, Sklenar P et al (2010) Genome size correlates with growth form habitat and phylogeny in the Andean genus Lasiocephalus (Asteraceae). Preslia 82:127–148

    Google Scholar 

  • Eilam T, Anikster Y, Millet E, Manisterski J, Sagi-Assif O, Feldmann M (2007) Genome size and genome evolution in diploid Triticeae species. Genome 50:1029–1037

    Article  PubMed  CAS  Google Scholar 

  • Galbraith DW, Harkins KR, Maddox JM, Ayres NM, Sharma DP, Firoozabady E (1983) Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science 220:1049–1051

    Article  PubMed  CAS  Google Scholar 

  • Greilhuber J (2005) Intraspecific variation in genome size in angiosperms: identifying its existence. Ann Bot 95:91–98

    Article  PubMed  CAS  Google Scholar 

  • Hamon P, Siljak-Yakovlev S, Srisuwan S et al (2009) Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: a revised view of species differentiation. Chromosom Res 19:291–304

    Article  Google Scholar 

  • Hodgson JG, Sharafi M, Jalili A et al (2010) stomatal vs genome size in angiosperms: the somatic tail wagging the genomic dog? Ann Bot 105:573–584

    Article  PubMed  CAS  Google Scholar 

  • Jakob SS, Meister A, Blattner RF (2004) The considerable genome size variation of Hordeum species (Poaceae) is linked to phylogeny life form ecology and speciation rates. Mol Biol Evol 21:860–869

    Article  PubMed  CAS  Google Scholar 

  • Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607

    Article  PubMed  CAS  Google Scholar 

  • Knight CA, Ackerly DD (2002) Variation in nuclear DNA content across environmental gradients: a quantile regression analysis. Ecol Lett 5:66–76

    Article  Google Scholar 

  • Knight CA, Beaulieu JM (2008) Genome size scaling through phenotype space. Ann Bot 101:759–766

    Article  PubMed  Google Scholar 

  • Lashermes P, Cros J, Combes M-C, Trouslot P, Anthony F, Hamon S, Charrier A (1996) Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. Theor Appl Genet 93(4):626–632

    Article  CAS  Google Scholar 

  • Lashermes P, Combes MC, Trouslot P, Charrier A (1997) Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor Appl Genet 94:947–955

    Article  CAS  Google Scholar 

  • Lashermes P, Combes MC, Robert J, Trouslot P, D'Hont A, Anthony F, Charrier A (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 261:259–266

    Article  PubMed  CAS  Google Scholar 

  • Leroy JF (1972a) Prospection des cafĂ©iers sauvages de Madagascar: deux espèces remarquables. Adansonia sĂ©rie 2 12: 317-328

    Google Scholar 

  • Leroy JF (1972b) Prospection des cafĂ©iers sauvages de Madagascar: sur deux espèces sympatriques du nord. Adansonia sĂ©rie 2 12: 345-358

    Google Scholar 

  • Leroy JF (1980) Evolution et taxogenèse chez les cafĂ©iers. Hypothèse sur leur origine. Comptes Rendus Hebdomadaires de l’AcadĂ©mie des Sciences de Paris, SĂ©rie D, 291:593-596

  • Louarn J (1972) Introduction Ă  l’étude gĂ©nĂ©tique des Mascarocoffea: nouvelles dĂ©terminations de leurs nombres chromosomiques. CafĂ© Cacao ThĂ© 26: 312-316

  • Louarn J (1993) Structure gĂ©nĂ©tique des cafĂ©iers africains diploĂŻdes basĂ©e sur la fertilitĂ© des hybrides interspĂ©cifiques (Proceedings of the 15th Congress of the International Scientific Association of Coffee Montpellier France) pp 243 -252, ASIC Paris France Publishers

  • Marie D, Brown SC (1993) A cytometric exercise in plant DNA histograms with 2C values for 70 species. Biol Cell 78:41–51

    Article  PubMed  CAS  Google Scholar 

  • Maurin O, Davis AP, Chester M, Mvung E, Jaufeerally-Fakim Y, Fay MF (2007) Towards a phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid dna sequences. Ann Bot 100:1565–1583

    Article  PubMed  CAS  Google Scholar 

  • Morley RJ (2000) Origin and evolution of tropical rain forests. John Wiley and Sons Ltd, Chichester

    Google Scholar 

  • Noirot M, Barre P, Louarn J, Duperray C, Hamon S (2000) Nucleus–cytosol interactions a source of stoichiometric error in flow cytometric estimation of nuclear DNA content in plants. Ann Bot 86:309–316

    Article  CAS  Google Scholar 

  • Noirot M, Poncet V, Barre P, Hamon P, Hamon S, de Kochko A (2003a) Genome size variation in diploid African Coffea species. Ann Bot 92:709–714

    Article  PubMed  CAS  Google Scholar 

  • Noirot M, Barre P, Duperray C, Louarn J, Hamon S (2003b) Effects of caffeine and chlorogenic acids on propidium iodie accessibility to DNA: consequences on genome size evaluation in coffee tree. Ann Bot 92:259–264

    Article  PubMed  CAS  Google Scholar 

  • Noirot M, Barre P, Duperray C, Hamon S, de Kochko A (2005) Investigation on the causes of stoichiometric error in genome size estimation using heat experiments: consequences on data interpretation. Ann Bot 95:111–118

    Article  PubMed  CAS  Google Scholar 

  • Ohri D, Bhargava A, Chatterjee A (2004) Nuclear DNA amounts of 112 species of tropical hardwoods—new estimates. Plant Biol 6:555–561

    Article  PubMed  CAS  Google Scholar 

  • Rakotomalala JJ (1992) DiversitĂ© biochimique des cafĂ©iers: Analyse des acides hydroxycinnamiques, bases puriques et diterpènes glycosides. ParticularitĂ©s des cafĂ©iers sauvages de la rĂ©gion malgache (Mascarocoffea Chev.). Thesis, Collection TDM, ORSTOM, Paris

  • Slovák M, Petr V, Urfus T, Suda J (2009) Complex pattern of genome size variation in a polymorphic member of the Asteraceae. J Biogeogr 36:372–384

    Article  Google Scholar 

  • Suda J, TrávnĂ­ÄŤek P (2006) Reliable DNA ploidy determination in dehydrated tissues of vascular plants by DAPI flow cytometry—new prospects for plant research. Cytom A 69:273–280

    Article  Google Scholar 

  • Wells NA (2003) Some hypotheses on the Mesozoic and Cenozoic paleoenvironmental history of Madagascar. In: Goodman S, Banstead J (eds) The natural history of Madagascar. University of Chicago Press, Chicago, pp 16–34

    Google Scholar 

  • Wendel JF, Cronn RC (2002) Polyploidy and the evolutionary history of cotton. Adv Agron 78:139–186

    Article  Google Scholar 

  • Yoder AD, Nowak MD (2006) Has vicariance or dispersal been the predominant biogeographic force in Madagascar? Only time will tell. Ann Rev Ecol Evol Syst 37:405–431

    Article  Google Scholar 

  • Zonneveld BJM, Leitch IJ, Bennett MD (2005) First nuclear DNA amounts in more than 300 angiosperms. Ann Bot 9:229–244

    Article  Google Scholar 

Download references

Acknowledgments

Razafinarivo NJ receives a PhD fellowship from IRD and benefits from the RubiComp IRD funds. The Ueshima Coffee Company (UCC) contributes to maintaining the field collection at Kianjavato, Madagascar. We thank FOFIFA authorities and all people who facilitated access and field work at the Kianjavato research station, Madagascar.

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Authors and Affiliations

  1. UMR DIADE, IRD, B.P. 64501, 34394, Montpellier cedex 5, France

    Norosoa J. Razafinarivo, Serge Hamon, Alexandre de Kochko, Valérie Poncet, Christine Dubreuil-Tranchant, Romain Guyot & Perla Hamon

  2. FOFIFA, B.P. 1444, Ambatobe, Antananarivo 101, Madagascar

    Jean-Jacques Rakotomalala

  3. Institut des Sciences du Végétal (IFR87), CNRS UPR 2355, Imagif, Centre de Recherche de Gif, bâtiment 23, 91198, Gif-sur-Yvette, France

    Spencer C. Brown & Mickael Bourge

  4. UMR DIADE, IRD, B.P. 50172, 97492, Sainte Clotilde cedex, La RĂ©union, France

    Emmanuel Couturon

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  1. Norosoa J. Razafinarivo
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  2. Jean-Jacques Rakotomalala
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  3. Spencer C. Brown
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  5. Serge Hamon
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  6. Alexandre de Kochko
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  7. Valérie Poncet
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  10. Romain Guyot
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Correspondence to Norosoa J. Razafinarivo.

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Communicated by D. Grattapaglia

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Razafinarivo, N.J., Rakotomalala, JJ., Brown, S.C. et al. Geographical gradients in the genome size variation of wild coffee trees (Coffea) native to Africa and Indian Ocean islands. Tree Genetics & Genomes 8, 1345–1358 (2012). https://doi.org/10.1007/s11295-012-0520-9

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