Table S5. Primer sequences, annealing temperature and functions of the 49 single copy nuclear genes used in this study.

Locus / Primer sequences (5'-3') / Alignment (bp) / Ta (°C) / Function annotation
exon / intron
PGN7 / F: CCCAATGCCCCCAGAGTTTT
R: AGCGAGGTGCTGCTTGAAGT / 441 / 336 / 54 / beta-amyrin synthase
PW3 / F: TTACAAGGCTGGGATGACTC
R: ATATGCCACCACTCCAACAA / 133 / 635 / 53 / 60S ribosomal protein
PW6 / F: CTGGTGCTCGGGTTCTGTAT
R: GGCTGAGCGACATCAGGAAA / 240 / 89 / 52 / mediator of RNA polymerase II transcription subunit 36a
PW7 / F: TGTTCCCGCTAGGTACAACT
R: CAACACCCTTTCCAGGCTTA / 285 / 529 / 54 / 5-methyltetrahydropteroyltriglutamate- homocysteine methyltransferase
PW8 / F: ATAGCTCGTGTAACTGATGG
R: TTGAGTGCGGGTGTCTGAAT / 124 / 371 / 64 / vesicle transport protein
PW13 / F: TGAAGAAGTCTGCCAAACCG
R: TGTCACCACCTCCAAACTCG / 165 / 457 / 50 / 40S ribosomal protein S10
PW22 / F: GTGCCGTTGAGTATGAAGAC
R: AGCTGCCTGAAGAAGTGCTA / 160 / 203 / 48 / cytochrome
PW26 / F: AAGAAGGGTAGCAAGAAAGG
R: CGTCAAGAATCCCAAGTCCA / 439 / 321 / 53 / magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase
PW28 / F: GGGGTGGGAATTTGGAAGTA
R: TGAAGGAGCATCGGAACCAT / 302 / 119 / 60 / photosystem I reaction center subunit VI
PW31 / F: TGTGAGCAAGGGATGAGGTT
R: AAGTGCAGATCACCCGAAGA / 164 / 120 / 50 / 50S ribosomal protein L2
PW32 / F: TTCTGACCCACCCAATCTTC
R: AGCCGCCTTTCGTAACTCTT / 0 / 332 / 46 / uncharacterized protein
PW35 / F: TCATCATTGACTCCACCACT
R: GAGATGGGGACAAAAGCAAT / 241 / 85 / 49 / elongation factor 1-alpha
PW39 / F: ACCACCAGTAGTACGATTCG
R: CAGGGGAGTTTGGGTTTGGA / 89 / 944 / 50 / ubiquitin-conjugating enzyme
PW41 / F: CACCAGGGTCGTATTATTCC
R: GAGAAGGTCGATTGCCAGAG / 99 / 917 / 48 / glucose-6-phosphate isomerase
PW47 / F: CGGAAGGTCGCTTTTACTCG
R: CAGGCTAATTTGCCCGCACT / 373 / 425 / 52 / OTU domain-containing protein
PW48 / F: CTGGTGCTCGGGTTCTGTAT
R: CTAGGCTTGAATTGATCTGC / 0 / 340 / 50 / uncharacterized protein
PW51 / F: GGATTCATGCTGAGAAGACC
R: GCACCTGGAAGAAGGATGTC / 144 / 1102 / 53 / 60S acidic ribosomal protein
PW53 / F: GGATTCATGCTGAGAAGACC
R: GCACCTGGAAGAAGGATGTC / 105 / 230 / 52 / photosystem II CP43 protein
PW54 / F: CCCCTAATCGAACTGTTTGG
R: CACTACTCTTCTCCGCATCA / 231 / 0 / 52 / ATP synthase CF1
PW59 / F: AACATTGCCGATAACCCCAC
R: CTGAGAGCACCAAAGAAATC / 262 / 116 / 52 / ribulose bisphosphate carboxylase/oxygenase activase
PW60 / F: CCAGTGTCCAACAACAATAG
R: GGAGGCAAATGTCGGTGAAA / 0 / 613 / 52 / uncharacterized protein
PW64* / F: AAGTAAAAACGGCGTGACCC
R: TTCCTCCCATTCTACCTGCT / 284 / 199 / 48 / ribulose bisphosphate carboxylase/oxygenase activase
PW65 / F: CAGAGGTAGTGAGCTTCTCA
R: AGCAGCAATAGTTAGCAGCC / 302 / 825 / 52 / uncharacterized protein
PW73 / F: AGGCGAGGAGAAGAGGATGA
R: CTCCGACTGAAACGATGCTC / 136 / 410 / 52 / vacuolar protein sorting-associated protein
PW76 / F: GATGCTTTGATGCCTTCTGG
R: CGTCTTTATCAGCGTCCTCT / 197 / 788 / 52 / SGF29 tudor
domain-containing protein
PW78 / F: CTGGCACCATCCGCAAAAAT
R: ACAGTTGTGAGACGAGGGTA / 0 / 1067 / 50 / uncharacterized protein
PW79 / F: CTCGCTTCTCACCAAGTCAG
R: ATGTCCTCCCCTTTGTTCTG / 303 / 150 / 50 / probable beta-1,4-xylosyltransferase
PW80 / F: TGCCAGTTATCAGGGCTCAA
R: TTTCCTTTCCTTCGCACTCC / 363 / 177 / 50 / photosystem I reaction center subunit N
PW83 / F: GTAGCAGAGGAGATGGGAAT
R: GAATCGTCAAACACAAAGGG / 366 / 562 / 52 / glutamate-cysteine ligase
PW85 / F: TGATGTGGAGAAGAGGAAGC
R: GCATAACACCGTCTGGCAGT / 157 / 240 / 52 / 40S ribosomal protein S27
PZ7 / F: ACCTGGTTCGCTGCTATTCC
R: CAAGCATTGGTTCCCTCTGG / 97 / 304 / 52 / PGR5-like protein
PZ8 / F: GGGAAGGAAAAGTTGCTCTG
R: TATTCGTGTTGGGGCATCTG / 263 / 539 / 54 / rossmann-fold NAD(P)-binding domain-containing protein
PZ14 / F: CTTTGTTTCTCCTCCTCCAG
R: GGATTTCCAGAGCAACCTTT / 178 / 667 / 54 / diacylglycerol kinase
PZ15 / F: TGAACAGGCATTATTACTCG
R: ACTCATCCTCCTCTTGAACG / 141 / 618 / 50 / 26S proteasome non-ATPase regulatory
PZ20 / F: GCAAAGAAAGGGGCAAATAC
R: TCACCACTGATCCCAACAAC / 201 / 86 / 51 / pyrophosphate-energized vacuolar membrane proton pump
PZ24 / F: GCAAAGAAAGGGGCAAATAC
R: TCACCACTGATCCCAACAAC / 138 / 846 / 54 / peroxiredoxin Q family protein
PZ26 / F: CCAAAGTGTCCTTGCTGCTC
R: TATTCTCCTCTGGTAGCCTG / 124 / 538 / 49 / oxidoreductase
PZ35 / F: TCAAGGTCTTTGTGGTGTT
R: TGCTTGCTTTGCTTTCTACC / 226 / 223 / 52 / Mediator of RNA polymerase II transcription subunit 18
PZ43 / F: CATCAAATGGAAGCGGAGAA
R: GGATAGGGTTATCGTCGTCA / 205 / 525 / 57 / ubiquitin carboxyl-terminal hydrolase
PZ46 / F: CCAAGCCCTAACAATAACGG
F: GTGTGTCATCTACAAAATCC / 248 / 123 / 50 / iron-sulphur cluster biosynthesis
family protein
PZ48 / F: CGAAGCTCCAAAGTTCAAAC
R: AACCTCTTGCCATCAAATCC / 107 / 600 / 50 / 40S ribosomal protein S25
PZ58 / F: GCTCACGCAAGCAGTGTATG
R: CTTCGTCAGATATTCCCGTC / 219 / 547 / 47 / F-box/RNI-like superfamily protein
PZ60 / F: TTGATGAACGAAGATAAGCG
R: ATTTGACTGACTGGTTTGGA / 126 / 474 / 52 / protein MEI2
PZ63 / F: TGTGGGAGATGATCTGCTGG
R: TTGGCAAGACGCTCTGACCT / 170 / 489 / 48 / phosphopyruvate hydratase family protein
PZ64 / F: GTGAGGATGGTGAGGGTAAG
R: TGATGCCAGCAGATGTAGTC / 337 / 338 / 49 / 40S ribosomal protein S15
PZ66 / F: GCTGAACGATGTATTTGCCA
R: CTTTGTCCAACGCTTCCTGC / 238 / 662 / 53 / beta-carotene hydroxylase
PZ67 / F: TTGACGCCGACTTTGACACC
R: GCATCACAACATCACCCTTA / 303 / 1052 / 50 / 4-hydroxy-3-methylbut-2-enyl
diphosphate reductase
PZ69 / F: GTGAGCAAGCTAAACATGGC
R: TAGGACCAGCAGCAAGGATT / 541 / 402 / 57 / phosphoenolpyruvate carboxy kinase
PZ70 / F: CGAGGCTGAAAAAGCATACT
R: TAGAGAGGAATCATTGGTTG / 261 / 369 / 50 / tetratricopeptide repeat protein

* PW59 and PW64 are different regions of the same gene.