Distribution of Pollen/Microspore F-Box Protein Genes Among Subfamilies

Supplemental Table 1

139 F-box protein genes presumably transcribed in uninucleate microspore and in the pollen (From (Honys and Twell 2003; Honys and Twell 2004; Pina et al. 2005) signal>50).Sub-families are indicated, except for the F-box protein genes not reported in (Gagne et al. 2002), or in the PlantsUBQ database( which are noted by a question mark. Known name and/or predicted function when reported are indicated in the last column. Tandem* indicates that the next/previous gene is also an F-box protein gene of the same sub-family, however not expressed in male gametophyte, unless noticed in the table.

Gene / Sub-family / Known name/predicted function
At1g06110 / C2 / SKIP16: SKP1/ASK Interacting protein 16
At1g06630 / B7
At1g10780 / C4
At1g10890 / A2
At1g12820 / C3 / AFB3: Auxin Signaling F-box 3
At1g13570 / B5
At1g16940 / B6 / Tandem*
At1g19930 / D
At1g21760 / C4 / FBP7
At1g22040 / D
At1g23780 / E / Tandem*
At1g30790 / A4 / Tandem* At1g30780 weak expression in UNM
At1g32430 / A1
At1g43640 / C4 / AtTLP5: tubby like protein 5
At1g47270 / C4 / AtTLP6: tubby like protein 6
At1g47340 / A5
At1g53320 / C4 / AtTLP7: tubby like protein 7
At1g53360 / A5 / Tandem*
At1g55000 / C2
At1g55030 / B4
At1g56610 / B2 / Syntaxin-related
At1g60570 / D
At1g61340 / C2
At1g63090 / E / AtPP2-A11: Phloem Protein 2-A11
At1g65760 / C5 / Inverted Tandem*
At1g67340 / E
At1g68050 / E / FKF1: Flavin-Binding Kelch Domain F-box protein
At1g70360 / E
At1g70590 / C4
At1g76900 / C4 / AtTLP1: tubby like protein 1
At1g78280 / E / transcription factor domain
At1g78750 / B6 / Tandem*
At1g78840 / B6
At1g80570 / C3
At2g01620 / C2 / MEE11: maternal effect embryo arrest 11
At2g02230 / E / AtPP2-B1: Phloem Protein 2-B1
At2g04230 / B4
At2g17030 / C5 / Tandem*
At2g17830 / A2
At2g21930 / A4
At2g29780 / D / Tandem* At2g29770 weak expression in UNM
At2g31470 / A5 / DOR
At2g38590 / A2
At2g41170 / E
At2g42720 / B7
At2g43260 / A3
At2g43270 / A3 / Putative myb related Transcription factor
At2g44030 / D
At2g44630 / D
At2g44900 / E / ARABIDILLO-1
At2g47900 / C4 / AtTLP3: tubby like protein 3
At3g03360 / B5
At3g06240 / A3
At3g06570 / D
At3g07550 / C3
At3g07870 / C4
At3g08810 / D
At3g12350 / E
At3g13680 / A2
At3g13820 / A2 / Tandem* At3g13830 weak expression in UNM
At3g14710 / B5
At3g16740 / A2
At3g17710 / A1
At3g18720 / C5
At3g18980 / A1 / ETP1
At3g20270 / ? / Lipid binding F-box related
At3g20620 / ? / F-box related
At3g20700 / A2 / Tandem*
At3g20710 / A2 / Tandem*
At3g21170 / A1
At3g22870 / A2
At3g24760 / A3
At3g28330 / A3
At3g50080 / C3 / VFB2/ VIER F-BOX PROTEINE 2
At3g51530 / ? / F-box related
At3g52030 / C4
At3g53000 / E / AtPP2-A15: Phloem protein 2-A15
At3g54480 / C3 / SKIP 5: SKP/ASK Interacting Protein 15
At3g54650 / C2 / FBL17
At3g58860 / B7
At3g59000 / B7 / B7 Cluster
At3g60350 / E / ARABIDILLO-2
At3g61340 / A5
At3g61590 / C5 / HWS/ HAWAIIAN SKIRT
At3g62230 / B5
At3g62430 / B3
At3g63220 / D
At4g00320 / B4 or B7
At4g00755 / ? / SKIP2/F-box related
At4g01640 / ? / F-box related
At4g02440 / C4 / EID1: EMPFINDLICHER IM DUNKELROTEN LICHT 1
At4g03030 / C5
At4g04690 / A1 / AtFBX15
At4g05460 / C5 / C5 Cluster
At4g05620 / D
At4g08980 / C2 / FBW2: F-box with WD-40 2
At4g10925 / ? / NTF2: Nuclear transport factor 2 family protein
At4g13960 / B7
At4g15475 / ? / AtFBL4
At4g21510 / C2
At4g22280 / ?
At4g23960 / E
At4g24210 / C2 / SLY1: SLEEPY1
At4g25710 / D
At4g26340 / B4 / Tandem*
At4g33210 / D / AtFBL15/SLOMO
At4g35930 / ?
At4g38870 / A4
At4g38940 / D
At4g39240 / D
At4g39550 / D / D cluster
At4g39570 / D / D cluster
At4g39753 / D / D cluster
At5g02910 / B5
At5g03000 / D
At5g03970 / A6
At5g15710 / C5
At5g18680 / C4 / AtTLP11
At5g18770 / B6
At5g18780 / B6
At5g21040 / C2 / FBX2
At5g22730 / B6 / B6 Cluster
At5g27750 / B6
At5g27920 / ?
At5g37040 / A1
At5g39250 / C2
At5g40470 / ?
At5g42360 / C5 / Tandem*
At5g44980 / B6
At5g45360 / C3
At5g49000 / D / D Cluster
At5g49610 / A3
At5g52620 / A5
At5g52880 / C2
At5g56180 / C3 / ARP8:ACTIN-RELATED PROTEIN 8
At5g60610 / B4
At5g63520 / C2
At5g65850 / A5
At5g67250 / C3 / SKIP2
VFB4:VIER F-BOX PROTEINE 4

Distribution of pollen/microspore F-box protein genes among subfamilies:

A1: 6/64; A2: 9/53; A3: 6/30; A4: 3/41; A5: 6/46; A6: 1/3 ; B1: 0/6; B2: 1/5; B3: 1/2; B4: 5/43; B5: 5/18; B6: 8/38; B7: 5/57; C1: 0/8; C2 12/18; C3: 8/22; C4 12/26; C5 8/66; D: 19/91; E 13/56; No Subfamily: 11

Supplemental Table 2

Summary of F-box protein genes expression from RT-PCR data.

Pollen specific / Expressed in pollen and/or flowera / Expressed in all tested tissues (sporophytic and gametophytic) / Expressed only in sporophytictissuesa / Not expressed
At4g04690 (A1)Spe
At3g17710 (A1)Spe
At5g41720 (A6)Com
At3g62230 (B5)Com
At4g13960 (B7)Spe
At3g58860 (B7)Spe
At3g18720 (C5)Com / At4g04690 (A1)Spe
At3g17710 (A1)Spe
At3g13680 (A2)Spe
At3g20710 (A2)Spe
At3g24760 (A3)Com
At3g28330 (A3)nd
At2g21930 (A4)nd
At4g38870 (A4)ColSpe
At2g31470 (A5) FlSpe
At5g03970 (A6) Com
At5g41720 (A6) Com
At1g67623 (A6) Com
At3g62230 (B5) Com
At4g13960 (B7)Spe
At3g58860 (B7)ColSpe
At1g47270 (C4) Com
At5g18680 (C4)Spe
At1g53320 (C4) Com
At1g70590 (C4) Com
At3g18720 (C5) Com
At4g03030 (C5) Com
At3g61590 (C5) Com
At3g06570 (D)Spe
At5g03000 (D)Spe
At3g08810 (D)Spe
At4g23960 (E)Spe / At3g20710 (A2)Spe
At3g24760 (A3) Com
At3g28330 (A3)nd
At5g03970 (A6) Com
At1g47270 (C4) Com
At5g18680 (C4)Spe
At1g53320 (C4) Com
At4g03030 (C5) Com
At3g61590 (C5) Com
At3g06570 (D)Spe
At4g23960 (E)Spe / At2g31470 (A5)FlSpe
At5g52620 (A5)ColSpe
At1g78750 (B6) Com
At1g10780 (C4) Com
At4g38940 (D)Spe / At5g37040 (A1) Ps
At3g13820 (A2)Spe
At3g61340 (A5)Spe
At2g44030 (D)Spe

(a)Col indicates expression in this accession only. Sporophytic expression may be found in both accessions (see Fig. 1). Fl=expression found in flowers only. The belonging to Common (Com), Lineage-specific (Spe) or Pseudo (Ps) FBXclasses according to (Hua et al. 2013; Hua et al. 2011) is indicated for each gene (see discussion). nd: not found in this grouping.

Supplemental Table 3-primers used-

Primers for transcriptdetection / Sequence 5’ to 3’
HistoneFor / TGGCTCGTACTAAGCAAACAG
HistoneRev / CACGTTCTCCTCTGATCCTG
At4g04690-LP / TACAGCGAACGTCAATGGCTT
At4g04690-RP / AAACGGGTCAAGGTAGCGAAA
At5g37040-LP / CTCCATTGCTTTAGATCCGTT
At5g37040-RP / CAAGGAATGGTGATCAAACTG
At3g17710-LP / TCCACCTCGATCTCTTGTTCG
At3g17710-RP / TGATGTGATTCAAAAGGAACCG
At3g13680-LP / CCAGGCGATTTGGTAGAGGAG
At3g13680-RP / CTTTTGCCCGGTTTGTTGATT
At3g13820-LP / GAGATTCTCTCAAGGACTCCG
At3g13820-RP / TTTTGTTCTTGTTGCTTTTGG
At3g20710-LP / GGGTTCCGTTTAAATACCTGA
At3g20710-RP / TAAGAAGATGCTCCACGACAC
At3g24760-LP / TCCTCTATCATCTCCCAATCC
At3g24760-RP / TAGACACCGTTGAGCAGAAAC
At3g28330-LP / AGGCAATGCGTAGAGATTCTT
At3g28330-RP / TGCTATGTTCCACATCCTTGT
At2g31470-LP / ACGAAAACTTTGAACCAATCC
At2g31470-RP / TTAACCTTAAACGCTCCCATT
At3g61340-LP / AGAAGAAGAGAAATCCGAACG
At3g61340-RP / TGGGTACAAGGTTAACATCCTC
At5g52620-LP / TCAATCGCTAAGTTTGGTCTC
At5g52620-RP / TTCTCTGACCCTTCAAAACCT
At5g03970-LP / TTGAGATTATAGCCAGCCCTT
At5g03970-RP / ATCTTGTAGCTACCGCTTGGT
At5g41720-LP / TCGTCATCTCCATAGAACCAA
At5g41720-RP / ATGATCTTATACCGAAACGGG
At1g67623-LP / GAGAGTAGAAACCCCGAAGC
At1g67623-RP / ATCGAAATTCCACCAACTCA
At3g62230-LP / CAGTCTCGTGACGTTGAAGTT
At3g62230-RP / CTCCAACATACGACCATAACG
At1g78750-LP / ATAAGCAACTTGCCAGAAACA
At1g78750-RP / CTTTATGGAATCATCCAAGCA
At4g13960-LP / ACAGTGTTCGTGTTGATTGGT
At4g13960-RP / CGATAAATTCACACACTTGGG
At3g58860-LP / ATATTCGCTGCCTTACGAGAT
At3g58860-RP / ACAATTTCAAGCCATTTAGGG
At1g47270-LP / AGATGTTGTTGCTTGTGCTTC
At1g47270-RP / CTTCTTGGACCTCTGGTTCTC
At5g18680-LP / CCTTCTTCCACCTAAAACTCG
At5g18680-RP / TCTCACTTTGCCAACATAAGC
At1g53320-LP / TGCCAGGTCCTAGAGACTTTT
At1g53320-RP / AACTGTTTCTTCATCGCCTTT
At1g10780-LP / TGATGCGATCCTTCAATACAT
At1g10780-RP / CAAGCGTGTTCATCTTCTGTT
At1g70590-LP / TTTTTGAAACCTCACGACAAG
At1g70590-RP / GAGTAACTGGTAGAGGACGCC
At3g18720-LP / AGTCAGAGAGGAGGACCAAAA
At3g18720-RP / GTTGGATGAGAGCTTTTCACA
At2g24540-LP / CAGGGGAAGCTTTTTGTACTC
At2g24540-RP / ACACTAAAATCCCCATTTTGC
At4g03030-LP / TAGATGGTGGTGAGAAATGGA
At4g03030-RP / CTCACACAACATGAACACCAA
At3g61590-LP / TGTCCCTGAAGCTGAATCATA
At3g61590-RP / CCAGTAAAGAGCTGAAGAGGG
At4g38940-LP / ATAATTAGGGCACCGAAGAAG
At4g38940-RP / AGCACAACAGCTACACAATCC
At3g06570-LP / AAGAAGAGGAAGATAGTGGCG
At3g06570-RP / ATCAAACCACAAAACTTTCCC
At2g44030-LP / ATCCCAATTGCTCAACTGTTG
At2g44030-RP / AAGGAATTGGAATCTGAATCG
At5g03000-LP / CATCATTCTCAATTTCCATCG
At5g03000-RP / ACACCAAATCTCCGTTTTACC
At3g08810-LP / ACTTCCCGATGATGTGCTATT
At3g08810-RP / GCAACAAGAACCTTCACAAGA
At4g23960-LP / CTCTGCCAGTTATCAATGACG
At4g23960-RP / CCGTTGAAGCACTTGACATAG
Primers for FST amplification
SK line / SK TAIL-L3:ATACGACGGATCGTAATTTGTCG
SALK lines / LB SALK 2:GCT TTC TTC CCT TCC TTT CTC
SAIL lines / LB3 SAIL: TAGCATCTGAATTTCATAACCAATCTCGATACAC
FLAG lines / TAG5: CTACAAATTGCCTTTTCTTATCGAC
TAG3: CTGATACCAGACGTTGCCCGCATAA
SK20342 / At3g17710-LP (seeabove) and SK TAIL-L3
SALK_109711 / ATGACGTTTGGAATATGCTGC and LB-SALK2
SALK_151018 / At3g20710-RP (seeabove) and LB-SALK2
SALK_151494 / ATCGGCGGATTAGTCGATATC and LB-SALK2
SALK_043730 / TCGAATACTAGTCGCCATTGC and LB-SALK2
SAIL_215_G12 / GGAATCCATTGCTTCTTCTCC and LB3 SAIL
SAIL_1236_G10 / TGCAATTGCATTGATGAAGAC and LB3 SAIL
SAIL_823_D11 / TGAATTCTCCGTTGGATTACG and LB3 SAIL
SALK_073805 / GGAAAAGGATTAATCTGTCTCTCC and LB-SALK2
SAIL_156_B04 / CAGAGAGGACGAGATCGTGAC and LB3 SAIL
FLAG_282G12 / TCATCTCCGCGATAAATTCAC and TAG5
SALK_149453 / TCGCATATGTTTGGGATAAGC and LB-SALK2
FLAG_530C06 / TCACTGGAAGAACATTCCAGG and TAG3
SALK_121520 / GACGATTCCGTTTCATTGATC and LB-SALK2
SALK_088349 / At3g61590-RP (see above) and LB-SALK2
FLAG_190E05 / AGGAGTTGACGACAATAATAAATTG and TAG5
SALK_078646 / CTAATCCTCGCTGGTTCACAC and LB-SALK2
SALK_019399 / GTTTACGGCTGAGGCTAAACC and LB-SALK2
FLAG_459H10 / AGTGGCTGGGTCATGATACTG and TAG5

Supplemental Table 4

Transmission through the pollen (TEM) of potential mutationsin F-box protein genes ruled out from the study (not expressed in pollen).

aMutant and WT progeny numbers are from genotyping; bA 1:1 segregation is expected if the TE is unaffected. The 2 upper limit is 3.83 for P= 0.05.

F-box protein gene
Subfamily, range / Insertion line / TEM / Observed mutant numbera / Total number of progeny (mutant + WT)a / Expectednumber of mutants if normal TEM(=total x 0.5) / 2 for a 1:1 segregationb
At4g04690A1, 46 / SAIL_1146 / 111.5 / 165 / 313 / 156.5 / 0,923
At5g37040A1, 49 / SALK_092219 / 106.6 / 144 / 279 / 139.5 / 0,290
At3g13820A2, 86 / SALK_096847 / 98.7 / 79 / 159 / 79.5 / 0,006
At2g31470A5, 209 / SALK_050074 / 94.8 / 91 / 187 / 93.5 / 0,134
At3g61340 A5, 216 / SALK_017388 / 81.2 / 95 / 212 / 106 / 2,283
At5g52620A5, 219 / SAIL_591_D07 / 79.0 / 83 / 188 / 94 / 2,574
At1g78750 B6, 342 / FLAG_482H06 / 110.1 / 98 / 187 / 93.5 / 0,433
At3g58860 B7, 401 / No mutant / nd
At1g47270C4, 462 / SALK_019494 (PROM) / 111 / 119 / 226 / 113 / 0,637
At5g18680C4, 464 / FLAG_441G06 (5’ UTR) / 98.4 / 62 / 125 / 62.5 / 0,008
At1g53320C4, 465 / SALK_092324 / 102.2 / 136 / 269 / 134.5 / 0,033
At1g10780 C4, 467 / FLAG_062G09 / 74.6 / 88 / 206 / 103 / 4,369
At4g03030 C5, 515 / SALK_121520 / 90.2 / 83 / 175 / 87.5 / 0,463
At4g38940 D, 581 / FLAG_077B08 / 104.5 / 92 / 180 / 90 / 0,089
At2g44030 D, 605 / SALK_041459 / 84.7 / 100 / 218 / 109 / 1,486

Gagne, J. M., B. P. Downes, S. H. Shiu, A. M. Durski and R. D. Vierstra, 2002 The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci U S A 99: 11519-11524.

Honys, D., and D. Twell, 2003 Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol 132: 640-652.

Honys, D., and D. Twell, 2004 Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol 5: R85.

Hua, Z., J. E. Pool, R. J. Schmitz, M. D. Schultz, S. H. Shiu et al., 2013 Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. Proc Natl Acad Sci U S A.

Hua, Z., C. Zou, S. H. Shiu and R. D. Vierstra, 2011 Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS One 6: e16219.

Pina, C., F. Pinto, J. A. Feijo and J. D. Becker, 2005 Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol 138: 744-756.