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. 2013 Oct 29;5(11):2155–2173. doi: 10.1093/gbe/evt162

Table 8.

Tandem Duplicate Genes in Arabidopsis and Aethionema GS Pathway Inventory

Protein Namea,b AGI α-Blockc AabIDd Syntelog % Identitye Lineage Specific? Col-0 → Aabf
Tandem duplicates of syntenic anchor genes retaining an At-α ohnolog
    UGT74C1 AT2G31790 A02N051 Aab37175 Yes 79.44 No 6 → 10
Aab37178 Yes 82.05 Aethionema 6 → 10
Aab37179 Yes 77.63 Aethionema 6 → 10
Aab37180 Yes 78.95 Aethionema 6 → 10
    UGT74D1_oa AT2G31750 A02N053 Aab37181 Yes 78.33 (no GS gene) 6 → 10
    [UGT-like] AT1G05670 A02N051 Aab31930 Yes 81.11 No 6 → 10
    UGT-like_oa AT1G05675 A02 Aab31932 Yes 71.4 (no GS gene) 6 → 10
    UGT74E2_oa AT1G05680 A02N053 Aab31933 Yes 59.8 (no GS gene) 6 → 10
    FMO-GSOX-2 AT1G62540 A03N117 Aab10869 Yes 76.6 No 11 → 8
    FMO-GSOX-3 AT1G62560 A03 Aab10867 Yes 71.9 No 11 → 8
    FMO-GSOX-4 AT1G62570 A03 Aab10866 Yes 55.2 No 11 → 8
    FMO-like_oa AT1G62580 A03 — — — (no GS gene) 10 → 7
    FMO-like_oa AT1G62600 A03 — — — (no GS gene) 10 → 7
    FMO-like_oa AT1G62620 A03 — — — (no GS gene) 10 → 7
    [FMO-like] AT1G12130 A03N117 Aab13543 Yes 65.09 No 11 → 8
    FMO-GSOX-5 AT1G12140 A03 Aab13546 Yes 71.9 No 11 → 8
    FMO-like_oa AT1G12200 A03 Aab13549 Yes 66.66 (no GS gene) 10 → 7
    CYP79F2 AT1G16400 A05N062 — — — Arabidopsis 8 → 9
    CYP79F1 AT1G16410 A05 Aab27579 Yes 72.79 Arabidopsis 8 → 9
    SOT16 AT1G74100 A05N186 Aab14278 Yes 91.07 No 3 → 3
    SOT18 AT1G74090 A05 Aab14277 Yes 83.9 No 3 → 3
    GSTU20 AT1G78370 A05 Aab07000 Yes 67.29 No 5 → 6
    GSTU23_oa AT1G78320 A05 Aab06994 Yes 81.74 (no GS gene) 5 → 6
    GSTU22_oa AT1G78340 A05 Aab06997 Yes 71.1 (no GS gene) 5 → 6
    GSTU21_oa AT1G78360 A05 Aab06998 Yes 76.71 (no GS gene) 5 → 6
    GSTU19_oa AT1G78380 A05N104 Aab06999 Yes 83.41 (no GS gene) 5 → 6
    [BCAT7] AT1G50090 A08N074 Aab22548 Yes 69 No 6 → 6
    BCAT-like_oa AT1G50110 A08 Aab22550 Yes 78.12 (no GS gene) 6 → 6
    [SUR-like] AT4G28420 A10N194 Aab31155 Yes 47.42 No 3 → 2
A10 Aab31154 Yes Aethionema
    SUR-like_oa AT4G28410 A10 Aab31153 Yes 63.96 (no GS gene) 3 → 2
    GGP1 AT4G30530 A10N314 Aab24374 Yes 87.6 No 5 → 5
    GGP-like_oa AT4G30540 A10 Aab24373 Yes 75 (no GS gene) 5 → 5
    GGP3_oa AT4G30550 A10 Aab24372 Yes 82 (no GS gene) 5 → 5
    [GGP-like] AT2G23960 A10N314 Aab11021 Yes 69.67 No 5 → 5
    GGP-like _oa AT2G23970 A10 Aab11018 Yes 83.6 (no GS gene) 5 → 5
    [IPMI-like] AT2G43090 A11N226 Aab19619 Yes 85.99 No 3 → 3
    IPMI2 AT2G43100 A11 Aab19630 Yes 78.71 No 3 → 3
    [BCAT5] AT5G65780 A19N002 Aab23605 Yes 75.3 No 6 → 6
    LINC4_oa AT5G65770 A19 Aab23607 Yes 70.08 (no GS gene) 6 → 6
    MYB29 AT5G07690 A26N034 Aab33585 Yes 65.13 Arabidopsis 6 → 4
    MYB76 AT5G07700 A26 — — — Arabidopsis 6 → 4
Tandem duplicates of genes inside the boundaries of α-blocks with nonretained At-αohnolog
    AOP1 AT4G03070 A01 Aab37231 Yes 70.03 Arabidopsis 2 → 1
    AOP3 AT4G03050 A01 — — — Arabidopsis 2 → 1
    GSTF10 AT2G30870 A02 Aab28612 Yes 91.59 No 4 → 4
    GSTF9_oa AT2G30860 A02 Aab28613 Yes 89.76 (no GS gene) 4 → 4
    CYP79C2 AT1G58260 A03 Aab17711 Yes 71.85 No 8 → 9
    CYP-like_oa AT1G58265 A03 Aab17712 Yes 60.71 (no GS gene) 8 → 9
    UGT74B1 AT1G24100 A05 Aab07827 Yes 80.65 Aethionema 6 → 10
A05 Aab07826 Yes 70.35 Aethionema 6 → 10
    CYP81F2 AT5G57220 A22 — — — Arabidopsis 2 → 1
    CYP71B10 _oa AT5G57260 A22 Aab25774 Yes 73.21 (no GS gene) 2 → 1
    BZO1 AT1G65880 A25 Aab31601 Yes 70.04 No 2 → 4
Aab31602 Yes 69.4 Aethionema 2 → 4
    BZO-like_oa AT1G65890 A25 Aab31603 Yes 68.85 (no GS gene) 2 → 4
Aab31604 Yes 67.83 (no GS gene) 2 → 4
Tandem duplicates of genes outside the boundaries of α-blocks
    MAM1 AT5G23010 — Aab12229 Yes 72.31 No 2 → 4
Aab12230 Yes 71.5 Aethionema 2 → 4
    MAM-L AT5G23020 — Aab12225 Yes 70.67 No 2 → 4
Aab12226 Yes 68.36 Aethionema 2 → 4
AtGS genes: 45% TD (29/64) AabGS genes: 46% TD (31/67) Ø 73.43%

aSquared brackets indicate ohnolog copies of GS biosynthetic genes without GO! annotation to GS biosynthetic process.

bThe “_oa” suffix indicates tandem duplicate copies without GO! annotation to GS biosynthetic process. These genes have not been considered for the tandem duplicate count of GS loci in both organisms.

cUnderlined items refer to offspring of one pre-α TD event.

dPredicted Aethionema CDS.

eIn case of Aethionema-specific TAR expansion, the corresponding Arabidopsis sequence for identity comparison was determined based on both genomic location and homology criteria.

fChange of gene family locus count in Arabidospsis → Aethionema order.