DNA sequences from type specimens and type strains - how to increase their number and improve their annotation in NCBI GenBank and related databases
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DNA sequences from type specimens and type strains - how to increase their number and improve their annotation in NCBI GenBank and related databases. / Renner, Susanne S.; Scherz, Mark D.; Schoch, Conrad L.; Gottschling, Marc; Vences, Miguel.
I: Systematic Biology, 2024.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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T1 - DNA sequences from type specimens and type strains - how to increase their number and improve their annotation in NCBI GenBank and related databases
AU - Renner, Susanne S.
AU - Scherz, Mark D.
AU - Schoch, Conrad L.
AU - Gottschling, Marc
AU - Vences, Miguel
N1 - Published by Oxford University Press on behalf of the Society of Systematic Biologists 2023. This work is written by (a) US Government employee(s) and is in the public domain in the US.
PY - 2024
Y1 - 2024
N2 - Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 1,000 species of arthropods, 8,441 vertebrates, and 430 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.
AB - Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 1,000 species of arthropods, 8,441 vertebrates, and 430 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.
U2 - 10.1093/sysbio/syad068
DO - 10.1093/sysbio/syad068
M3 - Journal article
C2 - 37956405
JO - Systematic Biology
JF - Systematic Biology
SN - 1063-5157
ER -
ID: 383619005