Nucleotidediversityandlinkagedisequilibriumat56stress-responseandphenologycandidategenesinEuropeanbeech(FagussylvaticaL.)

H.Lalagüe1,2,3,,K.Csilléry2,S.Oddou-Muratorio2,J.Safrana2,C.deQuattro3,B.Fady2,S.C.González-Martínez4,G.G.Vendramin3

1)ScuolaSuperioreSant'Anna,PiazzaMartiridellaLibertà33,56127Pisa,Italy

2)INRA,UR629EcologiedesForêtsMéditerranéennes(URFM),F-84914Avignon,France

3)PlantGeneticsInstitute,NationalResearchCouncil,ViaMadonnadelPiano10,50019SestoFiorentino(Firenze),Italy

4)DepartmentofForestEcologyandGenetics,NationalInstituteforAgricultureandFoodResearchandTechnology(INIA)-ForestResearchCentre(CIFOR),Madrid,Spain

Correspondingauthor:

G.G.Vendramin

CNR,PlantGeneticsInstitute,ViaMadonnadelPiano10,50019SestoFiorentino(Firenze),Italy

E-mail:

Tel:+390555225725

Fax:+390555225729

Appendix4.Listofthe58genesanddiversity,recombinationrateandLDestimates.

Seq.Name / Seq.Description / La / indelb / Sc / hapd / f.h_maxe / ρf / θπg / Dh / half.disti / Hj / num.pw.compk / prop.sig.ldl / mean.r2m / mean.log10recn
2 / c2-h2 zinc finger protein / 498 / na / 0 / na / na / na / 0 / na / na / na / na / na / na / na
4 / subtilisin-like protease / 711 / 1 / 5 / 4 / 0.86 / 0.08 / 0.47 / -1.31 / 0 / 0.26 / 10 / 10 / 0.07 / -4.1
7 / probable xyloglucan endotransglucosylase hydrolase protein 23 / 924 / na / 3 / 3 / 0.92 / 0.02 / 0.19 / -1.06 / 0 / 0.15 / 3 / 33 / 0.33 / -4.6
10 / adp-glucose pyrophosphorylase large subunit / 1177 / 2 / 22 / 18 / 0.1 / 7.43 / 2.98 / -0.37 / 0 / 0.97 / 231 / 37 / 0.12 / -2.1
14 / glutamate dehydrogenase 2 / 727 / na / 9 / 8 / 0.54 / 10.4 / 1.04 / -1.1 / 0 / 0.67 / 36 / 22 / 0.11 / -2
17 / short chain alcohol dehydrogenase / 1320 / na / 6 / 7 / 0.38 / 4.81 / 1.08 / 0.01 / 0 / 0.78 / 15 / 47 / 0.07 / -2.3
19 / histone h3 / 829 / 1 / 9 / 6 / 0.44 / 0 / 3.45 / 1.87 / 0 / 0.66 / 36 / 56 / 0.29 / -5.4
20 / beta-ketoacyl-coa synthase family protein / 861 / 1 / 4 / 3 / 0.41 / 0 / 1.86 / 2.18 / 0 / 0.66 / 6 / 100 / 0.44 / -5.4
21 / s-adenosylmethionine synthetase / 467 / na / 3 / 4 / 0.48 / 0.01 / 1.81 / 1.03 / 0 / 0.67 / 3 / 100 / 0.04 / -4.9
23-1 / ubiquinol-cytochrome c reductase iron-sulfur / 1299 / 1 / 35 / 16 / 0.24 / 20.63 / 6.35 / 1.18 / 30 / 0.92 / 595 / 47 / 0.12 / -1.6
24 / plastocyanin chloroplast / 515 / na / 6 / 7 / 0.28 / 0.01 / 2.84 / 0.86 / 0 / 0.82 / 15 / 47 / 0.05 / -5
27 / probable -trehalose-phosphate synthase / 544 / na / 5 / 6 / 0.66 / 0.03 / 1.27 / -0.48 / 0 / 0.54 / 10 / 10 / 0.03 / -4.5
30-2 / caffeic acid o-methyltransferase / 1331 / 4 / 38 / 10 / 0.31 / 6.44 / 0.95 / -1.59 / 188 / 0.86 / 703 / 43 / 0.19 / -2.2
33 / histone h4 / 520 / 1 / 4 / 3 / 0.76 / 0 / 2 / 0.92 / 0 / 0.38 / 6 / 50 / 0.51 / -5.4
39 / potassium transporter 2 / 480 / na / 3 / 2 / 0.55 / 0.01 / 3.1 / 3.06 / 0 / 0.5 / 3 / 100 / 0.99 / -4.9
47-1 / adenylate kinase / 999 / na / 9 / 8 / 0.66 / 38.38 / 0.22 / -1.6 / 0 / 0.55 / 36 / 8 / 0.02 / -1.4
50 / crt dre binding factor / 616 / 2 / 8 / 8 / 0.43 / 24.9 / 3.3 / 0.24 / 0 / 0.74 / 28 / 82 / 0.32 / -1.4
51-2 / isoflavone reductase homolog / 1091 / 1 / 17 / 7 / 0.43 / 3.78 / 2.38 / -0.47 / 489 / 0.72 / 136 / 57 / 0.28 / -2.4
52-1 / adenosylhomocysteinase s-adenosyl-l-homocysteine hydrolase / 522 / na / 12 / 5 / 0.44 / 0.01 / 10 / 3.73 / 0 / 0.71 / 66 / 94 / 0.56 / -5.3
52-2 / s-adenosyl-l-homocysteine hydrolase / 614 / na / 16 / 6 / 0.47 / 0 / 7.09 / 1.52 / 0 / 0.69 / 120 / 77 / 0.44 / -5.5
58 / cold regulated 413 plasma membrane 1 / 1135 / 1 / 11 / 10 / 0.63 / 5.18 / 1.43 / -0.45 / 60 / 0.58 / 55 / 33 / 0.15 / -2.3
60 / eukaryotic translation initiation factor 5-like / 756 / 2 / 14 / 13 / 0.21 / 1.27 / 3.58 / 0.14 / 0 / 0.87 / 91 / 38 / 0.07 / -2.9
61 / heat shock protein 70 / 920 / na / 5 / 5 / 0.38 / 0.01 / 1.98 / 2.05 / 0 / 0.7 / 10 / 90 / 0.25 / -5.3
62-1 / heat shock / 909 / na / 3 / 2 / 0.91 / 0.02 / 0.2 / -1.16 / 0 / 0.16 / 3 / 33 / 0.29 / -4.6
66 / s-adenosylmethionine decarboxylase / 1091 / na / 12 / 8 / 0.32 / 3.31 / 2.25 / 0.42 / 53 / 0.83 / 66 / 41 / 0.1 / -2.5
68-2 / glyceraldehyde 3-phosphate partial / 625 / na / 7 / 5 / 0.42 / 0.01 / 2.98 / 0.46 / 0 / 0.69 / 21 / 43 / 0.18 / -4.9
70 / pathogenesis-related thaumatin-like protein / 496 / na / 5 / 3 / 0.73 / 0.01 / 1.86 / 0.15 / 0 / 0.43 / 10 / 60 / 0.2 / -5
73 / formate dehydrogenase / 1308 / 1 / 13 / 9 / 0.28 / 3.76 / 2.38 / 0.04 / 149 / 0.82 / 78 / 64 / 0.18 / -2.4
80 / protein phosphatase 2c / 1359 / na / 9 / 8 / 0.34 / 3.29 / 1.67 / 0.53 / 0 / 0.79 / 36 / 47 / 0.12 / -2.5
88-1 / light-harvesting complex ii protein lhcb2 / 1315 / na / 4 / 4 / 0.78 / 0.28 / 0.62 / 0.31 / 0 / 0.36 / 6 / 100 / 0.88 / -3.5
88-2-1 / chlorophyll a b-binding protein / 621 / na / 7 / 5 / 0.73 / 0.01 / 1.03 / -1.03 / 0 / 0.44 / 21 / 48 / 0.34 / -5.2
88-2-2 / chlorophyll a b-binding protein / 698 / na / 6 / 5 / 0.47 / 11.86 / 0.83 / -1.02 / 0 / 0.69 / 15 / 13 / 0.08 / -1.9
91-2 / catalase / 1503 / na / 18 / 5 / 0.56 / 0.01 / 2.33 / -0.15 / 1384 / 0.56 / 153 / 54 / 0.43 / -5.1
92 / 1-aminocyclopropane-1-carboxylate oxidase / 774 / na / 7 / 8 / 0.48 / 0.17 / 2.09 / -0.2 / 0 / 0.7 / 21 / 33 / 0.11 / -3.8
98-1 / catalase / 1452 / 1 / 17 / 6 / 0.52 / 0.17 / 2.25 / 0.16 / 1365 / 0.61 / 136 / 96 / 0.46 / -3.8
99 / zinc finger (ccch-type) family protein / 418 / na / 2 / 2 / 0.9 / 4.15 / 0.41 / -0.69 / 0 / 0.18 / 1 / 0 / 0 / -2.4
100 / cryptochrome 1 protein 2 / 379 / na / 1 / na / na / na / 0.6 / na / na / na / na / na / na / na
102 / histone h3 / 1168 / 1 / 9 / 5 / 0.41 / 0.03 / 1.5 / 0.59 / 0 / 0.67 / 36 / 56 / 0.29 / -4.5
110-1 / cytosolic class i small heat-shock protein / 589 / na / 5 / 2 / 0.57 / 0.01 / 0.02 / 0.99 / 0 / 0.52 / 10 / 60 / 0.58 / -5
110-3 / heat shock protein / 679 / na / 2 / 3 / 0.9 / 0.02 / 0.39 / -0.3 / 0 / 0.19 / 1 / 100 / 0.37 / -4.7
123-1 / chlorophyll a b-binding protein / 674 / na / 8 / 5 / 0.73 / 0.01 / 0.77 / -1.44 / 0 / 0.44 / 28 / 21 / 0.13 / -5.1
123-2 / chlorophyll a b-binding protein / 698 / na / 6 / 6 / 0.4 / 0.02 / 1.57 / 0.13 / 0 / 0.7 / 15 / 33 / 0.09 / -4.6
125 / na / 411 / 2 / 6 / 5 / 0.47 / 0.01 / 3.75 / 0.97 / 0 / 0.71 / 15 / 60 / 0.18 / -5.1
129 / glyceraldehyde-3-phosphate dehydrogenase / 978 / na / 4 / 3 / 0.93 / 0.03 / 0.21 / -1.31 / 0 / 0.13 / 6 / 50 / 0.43 / -4.5
130 / ultraviolet-b-repressible protein / 518 / na / 9 / 3 / 0.77 / 0.01 / 5.52 / 1.47 / 0 / 0.37 / 36 / 78 / 0.77 / -5.2
131 / histone h3 / 618 / na / 8 / 10 / 0.32 / 21.45 / 0.07 / -1.08 / 0 / 0.8 / 28 / 36 / 0.18 / -1.6
132-1 / histone h4 / 496 / 1 / 4 / 3 / 0.81 / 0.01 / 1.53 / -0.16 / 0 / 0.32 / 6 / 50 / 0.49 / -5.1
133 / na / 918 / 1 / 11 / 9 / 0.28 / 0.01 / 2.4 / 0.27 / 135 / 0.84 / 55 / 40 / 0.18 / -4.9
134-2 / type 2 metallothionein / 993 / 2 / 12 / 20 / 0.2 / 20.02 / 0.95 / -0.59 / 0 / 0.91 / 66 / 24 / 0.11 / -1.6
142 / membrane protein cov / 501 / 1 / 17 / 13 / 0.21 / 0.18 / 3.47 / -0.88 / 0 / 0.89 / 136 / 57 / 0.44 / -3.7
145-2 / proteasome subunit alpha type-7 / 1254 / 2 / 26 / 12 / 0.27 / 0.9 / 4.94 / 0.75 / 108 / 0.84 / 325 / 42 / 0.16 / -3
148-1 / skp1-like protein / 1498 / 4 / 19 / 12 / 0.24 / 1.4 / 2.66 / 0.74 / 187 / 0.87 / 171 / 57 / 0.18 / -2.8
150-2 / auxin response factor 6 / 1304 / 3 / 16 / 9 / 0.3 / 1.14 / 4.01 / 1.06 / 666 / 0.8 / 120 / 78 / 0.3 / -3
154-1 / probable pectinesterase pectinesterase inhibitor 40-like / 1234 / na / 11 / 7 / 0.29 / 0.82 / 2.5 / 0.98 / 376 / 0.83 / 55 / 87 / 0.27 / -3.1
154-2-1 / pectin methylesterase / 700 / na / 3 / 3 / 0.66 / 0.01 / 1.37 / 0.98 / 0 / 0.46 / 3 / 67 / 0.32 / -5.2
155-2 / polygalacturonase-1 non-catalytic subunit beta / 1010 / na / 32 / 17 / 0.24 / 11.55 / 4.73 / -0.82 / 43 / 0.91 / 496 / 30 / 0.1 / -1.9
155-3 / polygalacturonase / 877 / na / 5 / 5 / 0.33 / 0.01 / 1.12 / -0.03 / 0 / 0.73 / 10 / 40 / 0.04 / -4.9
156 / udp-glucose 6-dehydrogenase / 967 / na / 5 / 4 / 0.59 / 0.01 / 0.49 / -0.52 / 0 / 0.58 / 10 / 60 / 0.24 / -5.2
average / 860 / 10 / 7 / 0.50 / 3.72 / 2.15 / 0.18 / 93 / 0.63 / 79 / 52 / 0.26 / -3.8

aConsensussequencelengthinbasepairs

bNumberofinsertions-deletionsevents

cNumberofsegregatingsites

dNumberofhaplotypes

eFrequencyofthemostcommonhaplotype

fComposite-likelihoodestimateofthepopulation-scaledrecombinationrate(;persite10-3)

gPopulation-scaledmutationrate(π;persite10-3)basedontheaveragenumberofnucleotidedifferences

hTajima'sD

iDistanceinbpbywhichther²isreducedbyhalf

jHaplotypediversity(H)

kNumberofpairwisepolymorphismsusedforr²

lNumber of significant pairwise r²

mmean value oflinkage disequilibrium misured by r²

nlogarithm of the pairwise-estimatesoftherecombinationrate to base 10.

Addendum: Genotyping an additional set of individuals from new populations and re-genotyping six of our 96 individuals with the KASPAR-LCG technology, we discovered that the four following gene pairs: 19 & 102, 33 & 132-1, 88-2-1 & 123-1, 123-1 & 88-2-2 are most likely the same genes. Their SNP order is identical and the mismatch rate between the individual genotypes is generally low (0% between 19 and 102; 2% between 33 and 132-1; and 4.6% between 88-2-1 and 123-1, and 123-1 and 88-2-2). In our data set, one gene per pair amplified better, thus had less missing data: these are genes 19, 33, 88-2-1 and 123-1-2. Nevertheless, we also kept genes102, 132-1, 123-1, and 88-2-2 in the Appendixes (mentioning this problem) and kept both primers for the four genes in GeneBank because (i) genes 102 and 123-1 each cover one additional SNP, and (ii) so far, we cannot entirely exclude the possibility that genes 33 and 132-1, 88-2-1 and 123-1, and 123-1 and 88-2-2 are real gene duplication events.

The Tables and Figures presented in the main text are not affected by the four duplicated genes (i.e. genes 102, 132-1, 123-1, and 88-2-2 are not among the 16 gene selected to present in the main text). The reported mean values of statistics over all genes, such the nucleotide diversity, stay the same to at least their fourth decimal place, after the removal of the four genes.

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