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Type material in the NCBI Taxonomy Database.

Federhen S - Nucleic Acids Res. (2014)

Bottom Line: Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species.For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria.This has important implications for many NCBI resources, some of which are outlined below.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA federhen@ncbi.nlm.nih.gov.

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Taxonomic distribution of sequence from type. Taken from the Tree view of the interactive taxonomy portlet on the sidebar of Nucleotide Entrez. (a) All type material. (b) Type material from eukaryotes other than fungi. (c) Type material from the animals.
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Figure 2: Taxonomic distribution of sequence from type. Taken from the Tree view of the interactive taxonomy portlet on the sidebar of Nucleotide Entrez. (a) All type material. (b) Type material from eukaryotes other than fungi. (c) Type material from the animals.

Mentions: Figure 2 shows the taxonomic distribution of sequences from type material in GenBank at several different levels. The vast majority are from the microbes—71% of our sequences from type are from the bacteria and 28% from the fungi, with 17K (1.8%) from the archaea and even 9K (0.9%) from the cyanobacteria (in spite of the code of nomenclature issues with this group). These numbers are inflated by WGS contigs, but they reflect the fact that type material is readily accessible for organisms that can be cultured. The middle panel shows the 2013 type sequences from eukaryotes other than fungi, generated by following the ‘more…’ hotlink near the bottom of the first portlet. Even at this scale most of these sequences are from cultures, the exceptions being the animals and the red algae. The final panel shows the distribution of type sequence from the animals. This pitifully small number is overwhelmingly from new species descriptions. While we may never see sequence from many of the existing type specimens in museums and herbaria, it is becoming increasingly common to include at least a little sequence data in new species descriptions (often a COI or matK/rbcL barcode)—often from the holotype specimen. It is also useful to preserve a tissue and/or DNA sample from the types, for future analysis.


Type material in the NCBI Taxonomy Database.

Federhen S - Nucleic Acids Res. (2014)

Taxonomic distribution of sequence from type. Taken from the Tree view of the interactive taxonomy portlet on the sidebar of Nucleotide Entrez. (a) All type material. (b) Type material from eukaryotes other than fungi. (c) Type material from the animals.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4383940&req=5

Figure 2: Taxonomic distribution of sequence from type. Taken from the Tree view of the interactive taxonomy portlet on the sidebar of Nucleotide Entrez. (a) All type material. (b) Type material from eukaryotes other than fungi. (c) Type material from the animals.
Mentions: Figure 2 shows the taxonomic distribution of sequences from type material in GenBank at several different levels. The vast majority are from the microbes—71% of our sequences from type are from the bacteria and 28% from the fungi, with 17K (1.8%) from the archaea and even 9K (0.9%) from the cyanobacteria (in spite of the code of nomenclature issues with this group). These numbers are inflated by WGS contigs, but they reflect the fact that type material is readily accessible for organisms that can be cultured. The middle panel shows the 2013 type sequences from eukaryotes other than fungi, generated by following the ‘more…’ hotlink near the bottom of the first portlet. Even at this scale most of these sequences are from cultures, the exceptions being the animals and the red algae. The final panel shows the distribution of type sequence from the animals. This pitifully small number is overwhelmingly from new species descriptions. While we may never see sequence from many of the existing type specimens in museums and herbaria, it is becoming increasingly common to include at least a little sequence data in new species descriptions (often a COI or matK/rbcL barcode)—often from the holotype specimen. It is also useful to preserve a tissue and/or DNA sample from the types, for future analysis.

Bottom Line: Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species.For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria.This has important implications for many NCBI resources, some of which are outlined below.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA federhen@ncbi.nlm.nih.gov.

Show MeSH