Table. 1 Chimeric 16S rDNA sequences detected in the public databases

Putative chimeric sequence (accession no.) 5' Parent sequence
 3' Parent sequence
 Approx. breakpoint (E. coli numbering) Reference study Chimera detection{ddagger}
Phylum (Class)* Closest BLAST match{dagger} Phylum (Class)* Closest BLAST match{dagger}
Inter-phylum
    Arctic96AD-3 (AF354607) Proteobacteria (Gamma) Arctic96AD-9 (AF354608) (98 %) Gemmatimonas BD7-2 (AB015578) (92 %) 935 Bano & Hollibaugh (2002) C, P
    Arctic95A-3 (AF355043) Proteobacteria (Delta) Arctic97A-12 (AF355044) (97 %) Marine group A Arctic96B-7 (AF355047) (91 %) 675 Bano & Hollibaugh (2002) C, P
    AT425_EubG1 (AY053495) OP1 KTK 32 (AJ133617) (87 %) Proteobacteria (Gamma) Pseudomonas sp. G2 (AF326356) (98 %) 1215 Lanoil et al. (2001) N
    BD7-9 (AB015584) Proteobacteria (Epsilon) BD7-6 (AB015582) (98 %) Actinobacteria BD2-10 (AB015539) (94 %) 1085 Li et al. (1999) S
    BPC043 (AF154080) Firmicutes BPC060 (AF154081) (98 %) OP9 GCA018 (AF154105) (98 %) 1070 Unpublished U
    BPC061 (AF154092) Planctomycetes Pirellula sp. Schlesner 516 (X81940) (90 %) Acidobacteria Sva0725 (AJ241003) (93 %) 990 Unpublished U
    BPC005 (AF154090) Proteobacteria (Delta) Desulfocapsa sulfexigens (Y13672) (94 %) Acidobacteria BPC015 (AF154085) (96 %) 930 Unpublished U
    BPC066 (AF154095) Acidobacteria wb1_A08 (AF317741) (93 %) Chloroflexi BPC110 (AF154084) (91 %) 875 Unpublished U
    d011 (AF422631) TM6 Ebpr8 (AF255643) (92 %) Firmicutes d154 (AF422677) (99 %) 380 Unpublished U
    MNB2 (AF293011) Proteobacteria (Alpha) Methylosinus sp. LW4 (AY007293) (90 %) Nitrospira MNC2 (AF293010) (98 %) 350 Stein et al. (2001) C
    MNF8 (AF293012) Nitrospira MNC2 (AF293010) (97 %) Proteobacteria (Gamma) SM2E06 (AF445725) (89 %) 1005 Stein et al. (2001) C
    MNA3 (AF293013) Nitrospira MNC2 (AF293010) (98 %) Proteobacteria (Gamma) Iron-oxidizer m-1 (AF387301) (93 %) 930 Stein et al. (2001) C
    UASB_TL84 (AF254390) Chloroflexi BPC110 (AF154084) (90 %) Proteobacteria (Delta) UASB_TL15 (AF254406) (99 %) 900 Wu et al. (2001a) C, S, P
    UASB_TL94 (AF254401) OP9 BA021 (AF323760) (94 %) Spirochaetes ‘Leptospira illini’ (M88719) (99 %) 1080 Wu et al. (2001a) C, S, P
    UASB_TL56 (AF254405) Proteobacteria (Delta) UASB_TL44 (AF254395) (99 %) OP8 OPB95 (AF027060) (98 %) 620 Wu et al. (2001a) C, S, P
    UASB_TL15 (AF254406) OP11 TA18 (AF229791) (99 %) Proteobacteria (Delta) UASB_TL11 (AF254397) (99 %) 930 Wu et al. (2001a) C, S, P
    VC2.1 Bac7 (AF068788) Aquificae VC2.1 Bac13 (AF068793) (99 %) Proteobacteria (Epsilon) VC2.1 Bac8 (AF068789) (99 %) 420 Reysenbach et al. (2000) C, H
    VC2.1 Bac9 (AF068790) Aquificae VC2.1 Bac13 (AF068793) (100 %) Proteobacteria (Epsilon) VC2.1 Bac8 (AF068789) (99 %) 420 Reysenbach et al. (2000) C, H
    VC2.1 Bac32 (AF068806) Proteobacteria (Epsilon) VC1.2-cl26 (AF367490) (98 %) Aquificae VC2.1 Bac10 (AF068791) (99 %) 1090 Reysenbach et al. (2000) C, H
    VC2.1 Bac43 (AF068810) Ferribacter DO008 (AF385508) (<94 %) Proteobacteria (Epsilon) VC2.1 Bac19 (AF068796) (99 %) 675 Reysenbach et al. (2000) C, H
    YNPFFP89 (AF391983) Acidobacteria SHA-18 (AJ249099) (93 %) Actinobacteria YNPFFP1 (AF391984) (96 %) 550 Unpublished U
Intra-phylum
    Arctic96B-6 (AF353224) Proteobacteria (Alpha) Arctic97A-1 (AF353228) (98 %) Proteobacteria (Alpha) Arctic96B-10 (AF353211) (99 %) 530 Bano & Hollibaugh (2002) C, P
    Arctic96BD-1 (AF354605) Proteobacteria (Gamma) Alcanivorax borkumensis (AF062642) (99 %) Proteobacteria (Gamma) Arctic96B-16 (AF354595) (99 %) 615 Bano & Hollibaugh (2002) C, P
    AT425_EubD5 (AY053489) Proteobacteria (Beta) AP009 (AY005030) (99 %) Proteobacteria (Gamma) BD5-14 (AB015570) (98 %) 555 Lanoil et al. (2001) N
    BD3-1 (AB015547) Proteobacteria (Gamma) BD3-6 (AB015548) (99 %) Proteobacteria (Gamma) BD5-14 (AB015570) (100 %) 790 Li et al. (1999) S
    BD6-4 (AB015574) Proteobacteria (Gamma) str. 61716 (AF227866) (99 %) Proteobacteria (Gamma) Shewanella violacea (D21225) (100 %) 520 Li et al. (1999) S
    BPC023 (AF154087) Proteobacteria (Gamma) Ebpr13 (AF255638) (94 %) Proteobacteria (Gamma) BPC028 (AF154088) (100 %) 1070 Unpublished U
    d035 (AF422644) Proteobacteria (Alpha) d163 (AF422687) (99 %) Proteobacteria (Alpha) d041 (AF422650) (99 %) 283 Unpublished U
    MNG7 (AF292997) Proteobacteria (Alpha) H34 (AF234750) (93 %) Proteobacteria (Alpha) MND8 (AF292999) (99 %) 1030 Stein et al. (2001) C
    MNH4 (AF293002) Proteobacteria (Beta) Tui3-12 (AF353297) (90 %) Proteobacteria (Alpha) Azospirillum sp. B510 (AB049111) (90 %) 550 Stein et al. (2001) C
    MNA5 (AF293005) Proteobacteria (Beta) A15 (AF234683) (95 %) Proteobacteria (Beta) MNC9 (AF293007) (98 %) 1165 Stein et al. (2001) C
    pIVWA101 (AB019722) Crenarchaeota (C1) 19H08 (AF393305) (99 %) Crenarchaeota (C1) pIVWA2 (AB019730) (99 %) 975 Takai & Horikoshi (1999) C
    SAGMA-C (AB050207) Crenarchaeota (C1) SAGMA-A (AB050205) (99 %)§ Crenarchaeota (C1) SAGMA-2 (AB050233) (98 %) 520, 790 Takai et al. (2001) C
    SAGMA-Z (AB050231) Crenarchaeota (C1) SAGMA-8 (AB050238) (96 %) Crenarchaeota (C1) SAGMA-2 (AB050233) (97 %) 720 Takai et al. (2001) C
    SAGMA-3 (AB050234) Crenarchaeota (C1) SAGMA-D (AB050208) (99 %) Crenarchaeota (C1) SAGMA-8 (AB050238) (96 %) 520 Takai et al. (2001) C
    TA07 (AF229780) Proteobacteria (Delta) BA053 (AF323776) (99 %) Proteobacteria (Delta) TA14 (AF229787) (99 %) 790 Wu et al. (2001b) N
    TA09 (AF229782) Proteobacteria (Delta) TA11 (AF229784) (99 %) Proteobacteria (Delta) Syntrophus gentianae (X85132) (99 %) 970 Wu et al. (2001b) N
    TA15 (AF229788) Proteobacteria (Delta) Syntrophus gentianae (X85132) (96 %) Proteobacteria (Delta) TA16 (AF229789) (96 %) 350 Wu et al. (2001b) N
    VC2.1 Arc7 (AF068818) Euryarchaeota (Thermococci) Thermococcus siculi (AJ291808) (99 %) Euryarchaeota (Thermoplasmata) vadinCA11 (U81778) (86 %) 935 Reysenbach et al. (2000) C, H

*Where possible, the nomenclature of the taxonomic outline for Bergey's Manual of Systematic Bacteriology (Garrity et al., 2001) has been used. Candidate phyla are named as described previously (Hugenholtz et al., 1998; Hugenholtz, 2002).

{dagger}Closest match to a sequence >1300 nt long.

{ddagger}Method(s) used by researchers who generated the sequence. C, CHIMERA_CHECK; H, long-range helical base pairing; S, signature nucleotide shift; P, partial treeing; N, none stated; U, unknown.

§A second breakpoint reintroduces this parent sequence at the 3' end.