<str<strong>on</strong>g>Proceedings</str<strong>on</strong>g> <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> <str<strong>on</strong>g>Third</str<strong>on</strong>g> <str<strong>on</strong>g>Internati<strong>on</strong>al</str<strong>on</strong>g> <str<strong>on</strong>g>C<strong>on</strong>ference</str<strong>on</strong>g> <strong>on</strong> <strong>Invasive</strong> SpartinaChapter 1: Spartina BiologyTable 2: Comparis<strong>on</strong>s <str<strong>on</strong>g>of</str<strong>on</strong>g> cDNA AFLP patterns in S. maritima, S. alternilflora, <str<strong>on</strong>g>the</str<strong>on</strong>g> hybrid S. x townsendii and <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid S. anglia. The followingselective primer combinati<strong>on</strong>s have been employed: EcoRI + ACG / MseI + CAA, EcoRI + ACG / MseI + CAC, EcoRI + ACA / MseI +CAA EcoRI + ACA / MseI + CAC EcoRI + AAC / MseI + CAA EcoRI + AAC / MseI + CA, EcoRI + AGA / MseI + CAG, EcoRI + AGA / MseI +CCA, EcoRI + ACC / MseI + CAA.Fragments inheritedin <str<strong>on</strong>g>the</str<strong>on</strong>g> hybridand <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploïdLost fragments in<str<strong>on</strong>g>the</str<strong>on</strong>g> hybrid andpresent in <str<strong>on</strong>g>the</str<strong>on</strong>g>allopolyploidLost fragments in<str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid<strong>on</strong>lyLost fragments in<str<strong>on</strong>g>the</str<strong>on</strong>g> hybrid and <str<strong>on</strong>g>the</str<strong>on</strong>g>allopolyploidM<strong>on</strong>omorphic fragments(173)127 30 14 2Polymorphicfragments(61)S. maritimaS. alteniflora28 2 13 410 0 4 0TOTAL 165 (70.5%) 32 (13.7%) 31 (13.2%) 6 (2.5%)(Liu and Wendel 2003). Epigenetic changes have been foundassociated with phenotypic instability in experimentally resyn<str<strong>on</strong>g>the</str<strong>on</strong>g>sizedallopolyploids (Comai et al. 2000; Kashkush etal. 2002). Using Methylati<strong>on</strong> Sensitive AFLP (MSAP),Salm<strong>on</strong> et al. (2005) have compared <str<strong>on</strong>g>the</str<strong>on</strong>g> methylati<strong>on</strong> patterns<str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> parental genomes <str<strong>on</strong>g>of</str<strong>on</strong>g> S. maritima and S. alterniflora, tothose <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> first generati<strong>on</strong> hybrid S. x townsendii and <str<strong>on</strong>g>the</str<strong>on</strong>g>resulting allopolyploid S. anglica. Thirty percent <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g>parental methylati<strong>on</strong> patterns were found altered in <str<strong>on</strong>g>the</str<strong>on</strong>g>hybrid and <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid, indicating that hybridizati<strong>on</strong>,ra<str<strong>on</strong>g>the</str<strong>on</strong>g>r than genome doubling have triggered most <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g>methylati<strong>on</strong> changes <str<strong>on</strong>g>of</str<strong>on</strong>g> S. anglica. This high level <str<strong>on</strong>g>of</str<strong>on</strong>g>epigenetic changes might explain <str<strong>on</strong>g>the</str<strong>on</strong>g> morphologicalplasticity <str<strong>on</strong>g>of</str<strong>on</strong>g> S. anglica and calls for fur<str<strong>on</strong>g>the</str<strong>on</strong>g>r investigati<strong>on</strong>s <str<strong>on</strong>g>of</str<strong>on</strong>g><str<strong>on</strong>g>the</str<strong>on</strong>g> potential regulati<strong>on</strong> <str<strong>on</strong>g>of</str<strong>on</strong>g> duplicate gene expressi<strong>on</strong>.In this perspective, transcriptomic changes in <str<strong>on</strong>g>the</str<strong>on</strong>g> hybridand <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid have been first analyzed using cDNAAFLP in order to examine whe<str<strong>on</strong>g>the</str<strong>on</strong>g>r <str<strong>on</strong>g>the</str<strong>on</strong>g> parental genomeshave different expressi<strong>on</strong> patterns in S. x townsendii and S.anglica. RNA was extracted from young leaves collected inindividual plants cultivated in <str<strong>on</strong>g>the</str<strong>on</strong>g> greenhouse, in S. maritima(collected in Guerande and Saint Armel, Brittany France), S.alterniflora (collected in Landerneau, Brittany, France), S. xtowsendii (Hy<str<strong>on</strong>g>the</str<strong>on</strong>g>, England) and S. anglica (collected inSaint Lunaire and Saint Armel, Brittany, France). Interindividualor inter-populati<strong>on</strong> variati<strong>on</strong> <str<strong>on</strong>g>of</str<strong>on</strong>g> cDNA AFLPpatterns was checked for each species and <strong>on</strong>ly stable,species-specific cDNA fragments were taken into accountfor comparis<strong>on</strong>s. Of <str<strong>on</strong>g>the</str<strong>on</strong>g> over 234 unambiguous fragmentsscored, 173 were found m<strong>on</strong>omorphic and 61 werepolymorphic (i.e., present or absent) between <str<strong>on</strong>g>the</str<strong>on</strong>g> parentalspecies. As AFLP markers are dominant, polymorphicfragments are expected to be present in <str<strong>on</strong>g>the</str<strong>on</strong>g> hybrid and <str<strong>on</strong>g>the</str<strong>on</strong>g>allopolyploid if expressi<strong>on</strong> <str<strong>on</strong>g>of</str<strong>on</strong>g> genome additivity isrespected. Loss <str<strong>on</strong>g>of</str<strong>on</strong>g> parental fragment is interpreted as a result<str<strong>on</strong>g>of</str<strong>on</strong>g> gene silencing, and appearance <str<strong>on</strong>g>of</str<strong>on</strong>g> fragments that areabsent in both parental species is interpreted as novel geneexpressi<strong>on</strong>. This genome-wide screening <str<strong>on</strong>g>of</str<strong>on</strong>g> duplicate geneexpressi<strong>on</strong> has been previously successfully employed to testgenome expressi<strong>on</strong> plasticity in various allopolyploids(Comai et al. 2000; Lee and Chen 2001; Kashkush et al.2002; Soltis et al. 2004; Adams et al. 2005). About seventypercent <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> parental fragments are inherited by both <str<strong>on</strong>g>the</str<strong>on</strong>g>hybrid and <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid (Table 2). Am<strong>on</strong>g <str<strong>on</strong>g>the</str<strong>on</strong>g> 61polymorphic fragments, 38 (28 from S. maritima and 10from S. alterniflora) were found to be additive in <str<strong>on</strong>g>the</str<strong>on</strong>g> hybridand <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid. Seventeen fragments (13 from S.maritima and 4 from S. alterniflora) are lost in S. anglica.All <str<strong>on</strong>g>the</str<strong>on</strong>g> fragments present in <str<strong>on</strong>g>the</str<strong>on</strong>g> hybrid and <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploidare already present in <strong>on</strong>e (or both) <str<strong>on</strong>g>the</str<strong>on</strong>g> parental species.When c<strong>on</strong>sidering both m<strong>on</strong>omorphic and polymorphicfragments between <str<strong>on</strong>g>the</str<strong>on</strong>g> parental species, <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploidhas lost 37 parental fragments <str<strong>on</strong>g>of</str<strong>on</strong>g> which 31 were still presentin <str<strong>on</strong>g>the</str<strong>on</strong>g> F1 hybrid S. x townsendii and 6 were lost in <str<strong>on</strong>g>the</str<strong>on</strong>g> hybridand <str<strong>on</strong>g>the</str<strong>on</strong>g> allopolyploid, which indicates an overall silencing inS. anglica <str<strong>on</strong>g>of</str<strong>on</strong>g> 15.8 % <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> examined loci, that occurredmostly following genome duplicati<strong>on</strong> in <str<strong>on</strong>g>the</str<strong>on</strong>g> polyploid.Although more loci have to be screened in Spartina to verify<str<strong>on</strong>g>the</str<strong>on</strong>g> extent <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> changes overall <str<strong>on</strong>g>the</str<strong>on</strong>g> genome, it appears fromthis first screening that 34.4 % <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> loci are silenced in S.anglica, when c<strong>on</strong>sidering <strong>on</strong>ly <str<strong>on</strong>g>the</str<strong>on</strong>g> parental fragments thatare polymorphic. This represents a c<strong>on</strong>sistent amount <str<strong>on</strong>g>of</str<strong>on</strong>g>changes compared to those recorded in o<str<strong>on</strong>g>the</str<strong>on</strong>g>r polyploidsusing similar methods. Kashkush et al. (2002) have reportedabout 2% alterati<strong>on</strong> <str<strong>on</strong>g>of</str<strong>on</strong>g> parental transcripts in experimentallyre-syn<str<strong>on</strong>g>the</str<strong>on</strong>g>sized allopolyploid wheat. Expressi<strong>on</strong> alterati<strong>on</strong>has also been found in allopolyploid Arabidopsis (Comai etal. 2000; Lee and Chen 2001). Recently, Soltis et al. (2004)found about 5% cDNA parental fragment loss and 4 % novelexpressi<strong>on</strong> in <str<strong>on</strong>g>the</str<strong>on</strong>g> allotetraploid Tragopog<strong>on</strong> mirus andTragopog<strong>on</strong> miscellus. Adams et al. (2003) showeddifferential expressi<strong>on</strong> patterns between homeologous genes-19-
Chapter 1: Spartina Biology<str<strong>on</strong>g>Proceedings</str<strong>on</strong>g> <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> <str<strong>on</strong>g>Third</str<strong>on</strong>g> <str<strong>on</strong>g>Internati<strong>on</strong>al</str<strong>on</strong>g> <str<strong>on</strong>g>C<strong>on</strong>ference</str<strong>on</strong>g> <strong>on</strong> <strong>Invasive</strong> Spartinain different tissues <str<strong>on</strong>g>of</str<strong>on</strong>g> allotetraploid cott<strong>on</strong> (Gossypium),suggesting that sub-functi<strong>on</strong>alizati<strong>on</strong> was c<strong>on</strong>sequent toallopolyploid formati<strong>on</strong>. Over 2000 transcripts werescreened by cDNA AFLP (Adams et al. 2004) and about 5%<str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> duplicated genes were inferred to have been silencedor down-regulated in <str<strong>on</strong>g>the</str<strong>on</strong>g> experimentally re-syn<str<strong>on</strong>g>the</str<strong>on</strong>g>sizedallotetraploid Gossypium.SUMMARY AND CONCLUSIONSAllopolyploid species represent two important outcomes<str<strong>on</strong>g>of</str<strong>on</strong>g> hybridizati<strong>on</strong> and genome duplicati<strong>on</strong> that are critical for<str<strong>on</strong>g>the</str<strong>on</strong>g>ir evoluti<strong>on</strong>ary success: Hybridizati<strong>on</strong> leads to <str<strong>on</strong>g>the</str<strong>on</strong>g> merger<str<strong>on</strong>g>of</str<strong>on</strong>g> two more or less differentiated genomes that havepreviously evolved independently and polyploidizati<strong>on</strong>entails an immediate duplicati<strong>on</strong> and functi<strong>on</strong>al redundancyat all loci. These events entail various molecular interacti<strong>on</strong>sand adjustments that have received much attenti<strong>on</strong> in <str<strong>on</strong>g>the</str<strong>on</strong>g>recent literature, as <str<strong>on</strong>g>the</str<strong>on</strong>g>y are now c<strong>on</strong>sidered as <str<strong>on</strong>g>the</str<strong>on</strong>g> keyprocesses that explain <str<strong>on</strong>g>the</str<strong>on</strong>g> evoluti<strong>on</strong>ary success <str<strong>on</strong>g>of</str<strong>on</strong>g> polyploidyin Eucaryotes (reviewed in Liu and Wendel 2003; Osborn etal. 2003). Heterosis and dosage effect in duplicated genomesare likely to increase <str<strong>on</strong>g>the</str<strong>on</strong>g> metabolic plasticity <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g>duplicated genes, <str<strong>on</strong>g>the</str<strong>on</strong>g>reby affecting <str<strong>on</strong>g>the</str<strong>on</strong>g> fitness <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> newlyformed species (Riddle and Birchler 2003).The particularly successful Spartina anglica ischaracterised by morphological plasticity and largeecological amplitude, c<strong>on</strong>trasting with a weak interindividualgenetic variati<strong>on</strong>, but c<strong>on</strong>sistent epigenetic andexpressi<strong>on</strong> plasticity <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> duplicated homeologousgenomes. Fur<str<strong>on</strong>g>the</str<strong>on</strong>g>r investigati<strong>on</strong>s and identificati<strong>on</strong> <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g>sequences that are affected by epigenetic regulati<strong>on</strong> andexpressi<strong>on</strong> changes should deepen our understanding <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g>ecological success <str<strong>on</strong>g>of</str<strong>on</strong>g> this young species. Spartina <str<strong>on</strong>g>of</str<strong>on</strong>g>fersparticular opportunities to learn about <str<strong>on</strong>g>the</str<strong>on</strong>g> evoluti<strong>on</strong>ary andecological c<strong>on</strong>sequences <str<strong>on</strong>g>of</str<strong>on</strong>g> polyploid speciati<strong>on</strong> andreticulate evoluti<strong>on</strong> at both <str<strong>on</strong>g>the</str<strong>on</strong>g> short term (in nascent speciessuch as S. anglica) and l<strong>on</strong>g term (in <str<strong>on</strong>g>the</str<strong>on</strong>g> parental, olderpolyploid species) <str<strong>on</strong>g>of</str<strong>on</strong>g> <str<strong>on</strong>g>the</str<strong>on</strong>g> evoluti<strong>on</strong>ary time scale.ACKNOWLEDGMENTSThis work is supported by CNRS funds (UMR CNRS6553 Ecobio), PICS 932 CNRS – CSIRO Canberra, NSF –CNRS funds (project 12 978), and by a postdoctoral grantfrom <str<strong>on</strong>g>the</str<strong>on</strong>g> French Ministry <str<strong>on</strong>g>of</str<strong>on</strong>g> Research to K. Fukunaga. Weare particularly grateful to Les Leunig and Paul Hedge for<str<strong>on</strong>g>the</str<strong>on</strong>g>ir assistance in sampling Australian populati<strong>on</strong>s <str<strong>on</strong>g>of</str<strong>on</strong>g> S.anglica in Victoria and Tasmania, respectively, to MikeMcCorry, for sending samples from Ireland, to TravisColumbus and Debra Ayres for sending various AmericanSpartina samples. J<strong>on</strong>athan Wendel and Keith Adams (IowaState University, Ames) are thanked for helpful assistance in<str<strong>on</strong>g>the</str<strong>on</strong>g> cDNA AFLP approach and stimulating discussi<strong>on</strong>s <strong>on</strong>polyploidy. Neil Bagnall (CSIRO Canberra) and SylvieBaloche (CNRS Rennes) are thanked for technical help.REFERENCESAbbott, R.J. and A.J. Lowe. 2004. 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Retrotranspos<strong>on</strong>s and genomic stability in populati<strong>on</strong>s <str<strong>on</strong>g>of</str<strong>on</strong>g><str<strong>on</strong>g>the</str<strong>on</strong>g> young allopolyploid species Spartina anglica C.E. Hubbard(Poaceae). Molecular Biology and Evoluti<strong>on</strong> 19: 1218-1227.-20-
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