CONTAMINANTS & PROBLEMATIC SEQUENCES

'A scientist is a shrinking violet if he/she made a mistake, and a roaring lion if he discovers a mistake by others.Albert Einstein
Nobody is perfect ... (please submit lacking information and tell us mistakes in the list!)

The lists below are outdated, but some sequences are still not corrected in the databases, and the problem still is acute.
Mislabelled or contaminant derived sequences must be corrected n the sequence depositories.


Authors are responsible for their sequences!
If there are doubts on the origin of sequences, or errors in sequences submitted, authors should use the respective interfaces
to correct the data and avoid the use of wrong data in scientific work! This information is especially necessary for people that are not so deeply involved in the respective field.

 

EMBL database: (see the EMBL update pages): "If you spot errors or inconsistencies in database entries not owned by yourself, first try contacting the authors so that they can update their sequences directly. If you are unsuccessful, then please also use the following form indicating third party update."


 

Papers (partly) reporting 'contaminants' rDNA sequences (Table 1 with sequence information see below)

Papers (partly) biased by 'contaminants data', e.g. by BLAST results caused by mislabelled sequences, or by 'incomplete' phylogenetic analyses

Table 2. Other gene sequences probably stemming from contaminants (based on Corradi et al. 2004) (Table 2 with sequence information see below)


Papers reporting sequence-affiliations later changed by species re-classification, or mislabelled sequences (Table 3 with sequence information see below)

Please note: under 'taxonomy' on this pages you find information about Glomeromycota species, including a species list with comments.

 

Table 1. rDNA sequences probably stemming from contaminants, July 2003

sequence

corrected
in data
-base?

most probable origin of sequence

originally proposed

origin of sequence

published

originally in

remark

U15692

NO

mite (Arachnida, Acari)

Gi. margarita

Waterman 1994

contaminant

U16755

NO

ascomycete

Gi. margarita

Waterman 1994

contaminant

U16756

NO

ascomycete

Gi. margarita

Waterman 1994

contaminant

U94713

NO ascomycete

En. infrequens

Millner et al. 2001 contaminant

U94714

NO ascomycete En. infrequens Millner et al. 2001 contaminant

AF004686

NO ascomycete Sc. coralloidea Millner et al. 2001 contaminant

AF006512

NO basidiomycete

Ac. lacunosa

Millner et al. 2001 contaminant

AF005060

NO basidiomycete

En. contigua

Millner et al. 2001 contaminant

AF005061

NO basidiomycete

En. contigua

Millner et al. 2001 contaminant

AJ541799

YES 08/03

Mortierella sp.

Acaulospora sp.

Carlsen et al. 2003

contaminant

AJ541798

YES 08/03

Mortierella sp.

Acaulospora sp.

Carlsen et al. 2003

contaminant

AF133777

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 4'

Pringle et al. 2000

contaminant

AF133778

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 4'

Pringle et al. 2000

contaminant

AF133779

YES

Uncultured ascomycete from Ac. colossica spore

Ac. colossica 'type 5'

Pringle et al. 2000

contaminant

AF133780

YES

Uncultured fungus from Ac. colossica spore, probably Umbellopsis-related

Ac. colossica 'type 3'

Pringle et al. 2000

contaminant

AF133781

YES

Uncultured fungus from Ac. colossica spore, probably Umbellopsis-related

Ac. colossica 'type 3'

Pringle et al. 2000

contaminant

AF133782

YES

Uncultured fungus from Ac. colossica spore, probably Umbellopsis-related

Ac. colossica 'type 3'

Pringle et al. 2000

contaminant

AF133783

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133784

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133785

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133786

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133787

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133788

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133789

YES

Uncultured fungus from Ac. colossica spore

Ac. colossica 'type 2'

Pringle et al. 2000

contaminant

AF133790

YES

Uncultured fungus from Ac. colossica spore (probably an ascomycete)

Ac. colossica 'type 6'

Pringle et al. 2000

contaminant

AF133791

YES

Uncultured fungus from Ac. colossica spore, Paraglomus or a basidiomycete?

Ac. colossica 'type 7'

Pringle et al. 2000

contaminant

 

Table 2. Other gene sequences probably stemming from contaminants (based on Corradi et al. 2004), March 2004

sequence

corrected
in data
-base?

origin of sequence

originally proposed

origin of sequence

published

originally in

remark

AJ133839
AJ133840
AJ133841
AJ133842

ascomycete ?

Gl. mosseae

Ferrol et al. 2000

H+-ATPase gene, GmHA1-4

AF158391

? Ac. laevis Rhody et al. 2003 b-tubulin gene

AF158400

? Sc. castanea Rhody et al. 2003 b-tubulin gene

AF159109

? Gl. mosseae Rhody et al. 2003 b-tubulin gene

U49665

?

Gi. rosea

Franken et al. 1997

b-tubulin gene

 

Table 3. rDNA sequences belonging to re-classified species, and sequences originally mislabelled with the wrong species affiliation in the database, July 2003

sequence

corrected
in data
-base?

origin of sequence

originally proposed

origin of sequence

published

originally in

remark

X58726

YES 05/03

Gigaspora rosea

Gi. margarita

Simon et al. 1992

species re-classification

AJ306445
AJ306446

YES 06/03

Scutellospora calospora

Sc. nodosa

Schler et al 2001b

species mislabelling

AJ239126

YES 03/03

Glomus claroideum

Gl. fistulosum (in sequence data base only, not in the publication)

Redecker 2000

Gl. fistulosum was synonymized with Gl. claroideum, was correctly given in the publication

AJ276083

YES 06/01

Glomus lamellosum

Gl. clarum

Schler et al 2001a

species re-classification

U36592

(was correct in databse)

Glomus sp.
According
to pers. comm. with J. Morton (originator of the isolate) the fungus once was supposed to be Glomus clarum. Now handled as Glomus sp. again, affiliation unclear and isolate lost.

Glomus sp. BR212

Simon 1996

was partly given as Glomus clarum, but species classification is unclear