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.'
"Ein Wissenschaftler ist eine Mimose, wenn er selbst einen Fehler gemacht hat, und ein brüllender Löwe, wenn er bei anderen einen Fehler entdeckt" Albert Einstein  
Nobody is perfect ... (please submit lacking information and tell us mistakes in the list!).

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 avoid the use of wrong data in scientific work! This information is especially necessary for people not so deep in the respective field.

The EMBL database rules (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)

• Carlsen T A, Sorensen S, Hoiland K (2003) A glomalean fungus (Zygomycota) from dead Norway Lemming Lemmus lemmus in South Norwegian Mountains, unpublished

• Waterman LD (1994) Sequence analysis of ribosomal DNA amplification products and investigations on protoplast isolation from vesicular-arbuscular mycorrhizal fungi of the genus Gigaspora. Thesis, Department of Biology, University of the West Indies

• Pringle A, Moncalvo J-M, Vilgalys R (2000) High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorhizal fungus Acaulospora colossica. Mycologia 92(2): 259-268
  Here, a BLAST search (30.06.2003) search for sequences (from the upper papers) probably erroneous annotated to be of glomeromycotan origin can be found

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• Millner PD, Mulbry WW, Reynolds SL (2001) Taxon-specific oligonucleotide primers for detection of Glomus etunicatum. Mycorrhiza 10: 259-265
  Here, a BLAST (17.07.2003) search for sequences (from the upper papers) probably erroneous annotated to be of glomeromycotan origin can be found

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• Clapp JP, Rodriguez A, Dodd JC (2001) Inter- and intra-isolate rRNA large subunit variation in Glomus coronatum spores. New Phytol. 149(3): 539-554

• Rodriguez A, Dougall T, Dodd JC, Clapp JP (2001) The large subunit ribosomal RNA genes of Entrophospora infrequens comprise sequences related to two different glomalean families. New Phytologist 152: 159-167

• Hijri M, Hosny M, van Tuinen D, Dulieu H (1999) Intraspecific ITS polymorphism in Scutellospora castanea (Glomales, Zygomycota) is structured within multinucleate spores. Fungal Genetics and Biology 26: 141–151

• Hosny M, Hijiri M, Passerieux E, Dulieu H (1999) rDNA units are highly polymorphic in Scutellospora castanea (Glomales, Zygomycetes). Gene 226: 61–71

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

• Chen DM, Cairney WG (2002) Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sites. Mycol Res 106: 532–540
  Here, a NCBI BLAST2 (29.06.2003) search of the sequences probably erroneous annotated to be of glomeromycotan origin can be found. The erroneous annotations were caused by mislabelled sequences in the database.

• Sanders IR (1999) No sex please, we’re fungi. Nature 399: 737–739

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

• Ferrol N, Barea JM, Azcón-Aguilar C (2000) The plasma membrane H+-ATPase gene family in the arbuscular mycorrhizal fungus Glomus mosseae. Curr. Genet. 37: 112-118

• Rhody D, Stommel M, Roeder C, Mann P, Franken P (2003) Differential RNA accumulation of two b-tubulin genes in arbuscular mycorrhizal fungi. Mycorrhiza 13: 137-142

• Franken P, Lapopin L, MeyerGauen G, Gianinazzi-Pearson V (1997) RNA accumulation and genes expressed in spores of the arbuscular mycorrhizal fungus, Gigaspora rosea. Mycologia 89: 293-297

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.

• Schüßler A, Schwarzott D, Walker C (2001b) A new fungal phylum, the Glomeromycota : phylogeny and evolution. Mycological Research 105: 1413-1421

• Schüßler A, Gehrig H, Schwarzott D, Walker C (2001a) Analysis of partial Glomales SSU rRNA genes: implications for primer design and phylogeny. Mycological Research 105: 5-15

• Redecker D (2000) Specific PCR primers to identify arbuscular mycorrhizal fungi (Glomales) within colonised roots. Mycorrhiza 10: 73-80 NOTE: the species name 'Gl. claroideum' was correctly given in the paper, the old name ('Gl. fistulosum') was used in the sequence database only (until May 2003)

• Simon L (1996) Phylogeny of the Glomales: Deciphering the past to understand the present. New Phytol. 133: 95-101

• Simon L, Lalonde M, Bruns TD (1992) Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots. Appl. Environ. Microbiol. 58: 291-295

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

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

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