1 / 22625 / Col-0 / United States / Columbia
2 / 22572 / Eden-1 / Sweden / Eden (Harnosand area)
3 / 22574 / Lov-1 / Sweden / Lovvik (Harnosand area)
4 / 22576 / Fab-2 / Sweden / Faberget (Harnosand area)
5 / 22578 / Bil-5 / Sweden / Billaberget (Harnosand area)
6 / 22580 / Var2-1 / Sweden / Varhallarna (Skane)
7 / 22584 / Omo2-1 / Sweden / Ostra Mocklo (Skane)
8 / 22586 / Ull2-5 / Sweden / Ullstorp (Skane)
9 / 22564 / RRS-7 / United States / North Liberty, Indiana
10 / 22566 / Knox-10 / United States / Knox, Indiana
11 / 22568 / Rmx-A02 / United States / St. Joseph, Michigan
12 / 22570 / Pna-17 / United States / Benton Harbor, Michigan
13 / 22596 / HR5 / United Kingdom / Ascot, Berks
14 / 22598 / NFA-8 / United Kingdom / Ascot
15 / 22600 / Sq-1 / United Kingdom / Ascot
16 / 22602 / CIBC5 / United Kingdom / Ascot, Berks
17 / 22612 / Uod-1 / Austria / Ottenhof
18 / 22588 / Zdr-1 / Czech Republic / Zdarec (Brno area)
19 / 22590 / Bor-1 / Czech Republic / Borky (Brno area)
20 / 22594 / Lp2-2 / Czech Republic / Lipovec (Brno area)
21 / 22592 / Pu2-7 / Czech Republic / Prudka, Croatia
22 / 22604 / Tamm-2 / Finland / Tammisari
23 / 22606 / Kz1 / Kazakhstan / Karagandy
24 / 22608 / Goettingen-7 / Germany / Goettingen
25 / 22610 / Rennes-1 / France / Rennes
26 / 22614 / Cvi-0 / Cape Verde / Cape Verde Islands
27 / 6788 / Lz-0 / France / Lezoux
28 / 6689 / Ei-2 / Germany / Eifel
29 / 6730 / Gü-0 / Germany / Glueckingen
30 / 22619 / Nd-1 / Germany / Niederzenz
31 / 22620 / C24 / - / -
32 / 22621 / N13 / Russia / Konchezero
33 / 22622 / Wei-0 / Switzerland / Weiningen
34 / 22623 / Ws-0 / Russia / Wassilewskija
35 / 22624 / Yo-0 / United States / Yosemite National Park
36 / 22626 / An-1 / Belgium / Antwerpen
37 / 22627 / Van-0 / Canada / University of British Columbia
38 / 6626 / Br-0 / Czech Republic / Brno (Brunn)
39 / 22629 / Est-1 / Russia / Estland
40 / 6732 / Gy-0 / France / La Miniere
41 / 22632 / Ra-0 / France / Randan, Puy-de-Dome
42 / 6608 / Bay-0 / Germany / Bayreuth
43 / 6714 / Ga-0 / Germany / Gabelstein
44 / 6796 / Mrk-0 / Germany / Markt/Baden
45 / 6800 / Mz-0 / Germany / Merzhausen/Ts.
46 / 6896 / Wt-5 / Germany / Wietze
47 / 22638 / Kas-2 / India / Kashmir
48 / 22659 / Ws-2 / Russia / Wassilewskija
49 / 22658 / Oy-0 / Norway / Oystese
50 / 22657 / Edi-0 / United Kingdom / Edinburgh
51 / 22656 / Bur-0 / Ireland / Burren
52 / 22655 / Ms-0 / Russia / Moscow
53 / 22654 / Kin-0 / United States / Kindalville, Michigan
54 / 22653 / Sorbo / Tadjikistan / Sorbo
55 / 22651 / Kondara / Tadjikistan / Khurmatov
57 / 22649 / Pro-0 / Spain / Proaza, Asturios
57 / 22647 / Ts-1 / Spain / Tossa del Mar
58 / 22645 / Fei-0 / Portugal / St. Maria d. Feiria
Supplemental Table 2. Primers utilized to obtain frequency and expression data using PCR and RT-PCR
Gene pair ID / Gene Pair / Primer ID(Fwd/Rev) / Forward Primer / Reverse Primer / Enzyme / Frequency / RT-PCR
1 / At2g39140 / 642/643a / 5’ GGCAATCAGTGAAGGCACA 3’ / 5’ CACTATACGCAGCCATGCTC 3’ / Mly / X
At3g43340 / 644/645a / 5’ CACGAAGGAAGAAATCATGAAG 3’ / 5’ CCCAAGATCTGAAGGAAGTCTG 3’ / HinfI / X
642/643 / 5’ AACTTCCCCAACCCTGTATAGC 3’ / 5’ CCCAGCATTTTTCACTAATTCC 3’ / DpnII / X
644/645 / 5’ AGTTGAGTTGATGCCAAAGC 3’ / 5’ TGTGGAGATACTTTGTCGTTCC 3’ / BccI / X
2 / At2g40955 / 722/723 / 5’ TCAAACATAGAGTTGTACCAAGAGC 3’ / 5’ CTCCATGTATGCTTTATTTGGAACC 3’ / XbaI / X / X
At4g15096
3 / At3g03700 / 630/631a / 5’ CCTCTTCCTCCTTCTTCTTCTCCC 3’ / 5’ TTTCTTGAGGTGGAAATGGTG 3’ / BccI / X
At3g04440 / 630/631 / 5’ CCACAACGTATTCAGCGTCTTC 3’ / 5’ CTTGTGCTTAATGTTGATAATGATTGTG 3’ / DpnII / X
[At3g03702] / 632/633 / 5’ CCCTGGAAGTGACTCTCTATGC 3’ / 5’ AGCCAATACACATGCCTGTAGC 3’ / DdeI / X
4 / At1g05090 / 638/639a / 5’ TAGGCACAACGACAACAGTTCCCAAG
TCTA 3’ / 5’ TGGAGGCACTGAAAGTTTGG 3’ / DdeI / X
At4g20720 / 638/639 / 5’ GGTTTCGGTACGATTGTCTGG 3’ / 5’ CGTTAAGGAATCTAGGGTTTGAGG 3’ / DpnII / X
640/641 / 5’ ATTGCTCGGACTCATCCTTCC 3’ / 5’ CGATCCATCGAGATTAAGAGAGG 3’ / RsaI / X / X
5 / At1g71920 / 626/627 / 5’ ATCGTTCTCCGCACATTTAGC 3’ / 5’ AGTATTTCCCGTTTGAGAGTGC 3’ / RsaI / X / X
At5g10330 / 628/629 / 5’ CAACCGTACAATGTCTCTGTTGC 3’ / 5’ TGCATCCATTCCAGATGTAACC 3’ / DdeI / X / X
6 / At1g49680 / 654/655 / 5’ TACCAAAGCGATCCAGATGACC 3’ / 5’ TCTCCATCAGAAGCTCTGTCTCC 3’ / BsmAI / X / X
At4g28870 / HpaII / X / X
At1g33460
7 / At1g18330 / 724/725 / 5’ TGACTCAATAACCAGCTCAGAAGC 3’ / 5’ TCAAGAGGTTTGGAACAACTGC 3’ / DpnII / X
At3g10113 / 724.1/725.1 / 5’ AATGCATTTGGCTCGGTTAC 3’ / 5’ TGAAGCTACCAGCGTCAATG 3’ / EarI / X
Table S2. (continued)
(Fwd/Rev) / Forward Primer / Reverse Primer / Enzyme / Frequency / RT-PCR
8 / At3g07380 / 683/684a / 5’ CAGTTTACTATTGAACTGATGCCTATG
AGTAGCC 3’ / 5’ TGTACGCCTATCGCGAATACAT 3’ / HpaII / X
At3g60990 / 685/686a / 5’ CAGTTTACTATTGAACTGATGCCTATG
AGTACTC 3’ / 5’ GTACGCCTATCGCGAATACA 3’ / DdeI / X
At5g48190 / 683/684 / 5’ CCATAACACGATTAGTTGTATATCTC 3’ / 5’ TTCTAATTTATGGAATGTATTATCGTG 3’ / AluI / X
685/686 / 5’ TTCGAGTTGAGAACGATTGG 3’ / 5’ AGACAATAACATTTATGAGGAGACC 3’ / AluI / X
687/688 / 5’ AATCAACAAAATAATTACACCATC 3’ / 5’ AACTGGTATAAATAATGATTGGAA 3’ / MlyI / X
9 / At2g19850 / 689/690 / 5’ GCTTTGGTTCTCTATTCCACACC 3’ / 5’ AGCTGAATTCGAAGTCCAATCG 3’ / DdeI / X / X
At3g54730 / 691/692 / 5’ ACAGCAGATCACCAAGTGTGC 3’ / 5’ CTCTCCAACAATGGAGAAATGG 3’ / MnlI / X / X
At4g04030 / 693/694 / 5’ CTTTTGGAACATGCCTTCGT 3’ / 5’ TACGAGATGTGAGAAAAACCTCAG 3’ / AluI / X / X
10 / At1g69750 / 656/657 / 5’ TTTTGTTTTCAGGAGAAGAAAGAAT 3’ / 5’ TCGATACGAGTACGACCCAAGT 3’ / BfaI / X
At1g66590 / 658/659 / 5’ GTAGAATGGCGGACATGATGC 3’ / 5’ AATTTCCTATCTCCTTTTCGTTGG 3’ / BfaI / X
11 / At3g28410 / 726/727a / 5’ GTCTCCTCTTTGAGCGAAGC 3’ / 5’ AGTTTGGACCTTGAGCGTTG 3’ / HinfI / X
At5g02700 / 726.1/727.1 / 5’ AATATCGCCGCACAGGAC 3’ / 5’ TGGTTTCCCCAACAGTAAGC 3’ / RsaI / X
726/727a / 5’ TGCTTAAAAGGGTCATTAGTCG 3’ / 5’ GTTGATGAAATCTGCACCATCG 3’ / BccI / X
12 / At2g46720 / 728/729 / 5’ CTCTCGTCCATGATCGTAAACC 3’ / 5’ GTCGTTGCCTCGATACATGC 3’ / NA / X / X
At3g10280 / (indel)
13 / At3g49420 / 660/661a / 5’ AGGATTTGGCGTATTCTTCTCGTTTTT
GGGAATAGAATT 3’ / 5’ GATAGGCCACCCGATGATAA 3’ / EcoRI / X
At5g01430 / 660/661 / 5’ TGGCAGCAAAAGGTAGAAGTAGC 3’ / 5’ CCCAAAAACGAGAAGAATACGC 3’ / RsaI / X
662/663 / 5’ GCAGCAAAAGGTAGAAGTAGC 3’ / 5’ CTGAAACTAAATGGGGTTCC 3’ / DpnII / X
14 / At5g43490 / 671/672a / 5’ CTGCTTCTGAGGTGCAAGG 3’ / 5’ CATCAATCTCTGGCAACAGC 3’ / BccI. BpmI / X
At5g48610 / 671/672 / 5’ TCCAATGCCTGCTTCTGAGG 3’ / 5’ GGCAACAGCTCCCTTGTAGG 3’ / HpyCH4IV / X
BccI
Table S2. (continued)
(Fwd/Rev) / Forward Primer / Reverse Primer / Enzyme / Frequency / RT-PCR
15 / At2g03330 / 675/676a / 5’ TCTGATTCCAGGGATTTTAGC 3’ / 5’ AACGGTGTTATACCCCAAGC 3’ / DpnII.BsaI / X
At3g11810 / 673/674 / 5’ aacgaatcatcaacgcacactc 3’ / 5’ CGGTGATAACAACGATGAAACC 3’ / BccI / X
675/676 / 5’ CGTCACTTCCTAGCTCTCTCC 3’ / 5’ CTGCAGAGTTCAATTTCACAGG 3’ / HpyCH4IV / X
16 / At4g00020 / 646/647 / 5’ TTAGAGACGGCTGCTGAACC 3’ / 5’ TCACCTAAACCAGCGTCTTCC 3’ / BccI / X / X
At5g01630 / 648/649a / 5’ TAGAGACGGCTGCTGAACCT 3’ / 5’ CTTAAGCTCGTCAGGCCAAC 3’ / DpnII / X
648/649 / 5’ CGATACTGACAGCGAAGAAGGAG 3’ / 5’ Cctgaggttcagattgaagcag 3’ / DpnII / X
17 / At1g15910 / 732/733 / 5’ ATCAGCGAGTCAGAGATTGAGG 3’ / 5’ AACCTTTGGAAACCCCAGTAGC 3’ / BsmAI / X / X
At4g00380
18 / At1g20600 / 650/651 / 5’ TTATCGAAGGAGCAAGTGAAGG 3’ / 5’ ACCATAATCTGCCACAAACTGC 3’ / BccI / X / X
At4g03170 / 652/653 / 5’ GTTATCGAAGGAGCAAGTGAAGG 3’ / 5’ ACAGGTGTTTTATCCCCATTCC 3’ / DpnII / X / X
19 / At2g10560 / 677/678 / 5’ GTCAGACCCATCTGTGTTGTCC 3’ / 5’ ATAAGCATCGTGGTTCACAAGG 3’ / MnlI / X / X
At5g04860 / 679/680 / 5’ TTCATCGGGTTTTTCCATCCAGAG 3’ / 5’ CACAGGTTCGCTTGCCGACTC 3’ / DpnII / X / X
a / At1g07920
[EF1a] / 5’ TGGTTTTGAGGCTGGTATCTCC 3’ / 5’ TGACCTGGGAGGTGAAGTTAGC 3’ / X
a indicates primer was redesigned for expression analyses
Figure S1. Examples of gel analysis of RT-PCR products for gene expression analyses. Digested (enzyme indicated) and undigested (uncut) RT-PCR products were run alongside EF-1a RT-PCR product. In addition, each gel includes PCR products (undigested and digested) from genomic DNA (indicated by a “G”). A) ID1: an example of asymmetrically expressed duplicates in which one gene was not expressed (corresponds to Figure 1A). B) ID14: an example of asymmetrically expressed duplicates in which one gene was expressed at lower levels (corresponds to Fig. 2E and 2F [reciprocal]). C) ID 16: an example of duplicate genes in which both genes are equally expressed. For each duplicate pair, the expected sizes for each locus are indicated and the bands identified on the gel according to their progenitor (p) or daughter (d). Note for ID16 (B), the size of the RT-PCR bands are 68bp less than the genomic PCR bands due to the presence of an intron in the amplified genomic sequence and each image is the merger of the top and bottom half of a single gel. The brightness level of the raw images has been increased for this figure to increase visibility of bands. Tissues are indicated by abbreviations: G=genomic DNA; RL=rosette leaves; CL=cauline leaves; YF=young flowers; OF=open flowers; ST=stems; R=root; Si=siliques; -RT=minus reverse transcriptase controls.
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