GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

Prosanta Chakrabarty,Melanie Warren,Lawrence Page,Carole Baldwin

doi:10.3897/zookeys.346.5753

Abstract

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the “Genetypes” naming system, which some have been reluctant to adopt because of the use of the “type” suffix in the terminology. In the new nomenclature, genetic sequences are labeled “genseq,” followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types – “genseq-1,” secondary types – “genseq-2,” collection-vouchered topotypes – “genseq-3,” collection-vouchered non-types – “genseq-4,” and non-types that lack specimen vouchers but have photo vouchers – “genseq-5.” To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital “G” and “S” when referring to the nomenclatural program) to provide a searchable tag (e.g., “genseq”; note lowercase “g” and “s” when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made.

Highlights

The use of genetic sequences has been increasing with each passing year (Benson et al 2005; Strasser 2011); the separation between voucher specimens and genetic sequences is growing
Of the remaining 34 publications there was either no clear link between catalog numbers of vouchers and sequences, or, rarely, it was made clear in the paper that no types were among those sequenced
Type materials remain essential for taxonomic comparisons, but sequence data from type materials have not been fully incorporated into these comparisons

Summary

Introduction

The use of genetic sequences has been increasing with each passing year (Benson et al 2005; Strasser 2011); the separation between voucher specimens and genetic sequences is growing. GenBank and other depositories are excellent sources of genetic sequences that have a strong system for accurately identifying genetic data being submitted (e.g., COI cannot be mislabeled as 16S), but little is done to check the accuracy of the identity of the organism from which the sequences were obtained (Federhen et al 2009). Erroneous identifications are difficult to discover, and the perpetuation of the error in subsequent uses of the sequence data is nearly impossible to stop. An identification may be questioned if a BLAST (Basic Local Alignment Search Tool, in GenBank) search or phylogenetic analysis reveals a sequence to be in an unexpected region of a similar species or in an unexpected part of a phylogeny

Methods

Results

Conclusion