Abstract
BackgroundDuring the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed.ResultsA Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service , users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available.DiscussionThe ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets.
Highlights
During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, so for species that are minute or otherwise lack distinct, readily obtainable morphological characters
It is sometimes possible to establish a hyphal connection between the fungal mycelium of the root tips and nearby fungal fruiting-bodies [5]; traditional fungal taxonomy rests to a large extent on the morphology of fruiting-bodies or other spore producing structures, and there is abundant literature information available for many groups of fungi
The present study introduces emerencia, a Perl script package to facilitate the keeping track of the identity of insufficiently identified GenBank sequences over time
Summary
During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. The traditional approaches to identification of mycorrhizae include studies based on light microscopy, isozyme assays, mating behaviour experiments, and somatic compatibility tests. All of these are associated with drawbacks such as low to moderate precision, high time consumption, or the requirement that the fungus be isolated and grown in culture, which is impossible for many mycorrhizal fungi [1,2,3,4]. This is reflected in the large number of root-associated fungi for which fruiting-bodies have never been found, suggesting that any attempt to characterize the below-ground mycoflora through collection and identification of above-ground fruiting-bodies is likely to give a skewed and incomplete picture [6,7,8]
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