Recent changes to the classification in the NCBI taxonomy database

Viral names
Brachiopod classification
Mosses
Takifugu and Fugu
What are the Euteleostomi?
Sharks and rays

Viral names

November 2021.

Recommendations for choosing a virus or phage name when submitting to GenBank.

The following text contains recommendations for choosing a name for a new phage or virus when submitting to GenBank. It has to two parts. The first part deals broadly with good naming principles when choosing the name for a virus or phage that has not yet been formally recognized by the ICTV while the second part specifically addresses metagenomic viruses and phages.

General suggestions for choosing a virus name when submitting to GenBank

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When choosing a name for a new phage or virus, please check first whether the name is already in use at GenBank or the ICTV. A prexisting name should not be used for an unrelated new virus. Similarly, it is recommended that the name for a new virus should not be different from a prexisting name by a single hyphen or another punctuation mark, because a name like 'Lizard virus XYZ-17' is likely to cause confusion if there is already another virus by the name 'Lizard virus XYZ17'.

If no specific name is desired, a sp. name based on a valid ICTV taxon name like e.g. 'Sapovirus sp.' is acceptable. However, if a unique name is desired, it is recommended to avoid names that are composed solely of the name of a host or locality and a taxon name. A name like 'Mouse cyclovirus' will likely in the course of time include several unrelated cycloviruses that just happen to be found in a mouse. Adding a number like e.g. 'Lizard parvovirus 1' adds more specificity but if there is more than just one parvovirus in lizards, it can also become ambiguous. A name with a complex unique identifier like e.g. 'Lizard virus XYZ17' on the other hand is very unlikely to be inadvertently duplicated.

Please avoid the use of word 'like' in the virus name. If you are not sure whether your virus belongs into the genus Ourmiavirus, instead of calling it 'Ourmia-like virus XY17', you can use the next higher formal taxon name, e.g. 'Botourmiaviridae XY17'. Also avoid the use of the word 'unclassified' in virus names. Instead of e.g. 'Sisal-associated Unclassified virus A', name it just 'Sisal-associated virus A' and it will be classified within the unclassified viruses in the GenBank taxonomy database.

For phage names, the ICTV standard name format is '[host genus] phage [ID]'. The specific epithet of the bacterial host species is not included in the phage name e.g. 'Escherichia phage CBA120' not 'Escherichia coli phage CBA120'. If the identity of the host bacterium is unknown, the phage name can consist of just the word 'Phage' and an unique identifier (e.g. 'Phage LM4'). The usage of the word 'virus' in the name of bacterial virus names is reserved for the species names of bacterial viruses that are created and recognized by the International Committee on Taxonomy of Viruses (ICTV) and published in the Virus Metadata Resource (VMR). For non-ICTV names, the word 'phage' is to be used.

In addition to the viral organism name, identifying information can be provided on the /isolate qualifier of the GenBank record and a wide variety of lab designations, localities, dates, host or personal names or abbrevations can be combined into a unique string as e.g. /isolate="bat/Berlin/XYZ-58/2021". Note however, that locality information alone (e.g. Maryland) does not provide a meaningful isolate qualifier. Instead, locality information should be fielded on the /country qualifier as e.g. /country="USA:Maryland".

Suggestions for naming of metagenomic viruses and phages for GenBank submissions

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Sequences from metagenomic sets can be submitted to GenBank in the organism name format 'Taxon sp.' where Taxon is the formal ICTV name ranked genus or higher that submitters can safely indentify for their sequences. Example would be 'Sapovirus sp.', 'Siphoviridae sp.' or 'Cressdnaviricota sp.'. Metagenomic viruses and phages can also be given individual names which is recommended in particular for viruses of medical importance, unique names that have been used in publications, or for otherwise individually characterized viruses.

GenBank will place 'Taxon sp.' names into unclassified bins reserved for non-ICTV names such that e.g. 'Sapovirus sp.' is found within 'unclassified Sapovirus', 'Siphoviridae sp.' in 'unclassified Siphoviridae', 'Cressdnaviricota sp.' in 'unclassified Cressdnaviricota'. In the GenBank record, metagenomic sequences receive the /metagenomic, /metagenome_source="text" and /environmental_sample source qualifiers.
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Brachiopod classification

The brachiopod section of the taxonomy database has been revised. The brachiopod classes Inarticulata and Articulata are no longer used in the classification because the Inarticulata are not recognized as monophyletic in recent cladistic analyses. A monophyletic Brachiopoda is recognized comprising four subphyla: Craniiformea, Linguliformea, Rhynchonelliformea, and Phoroniformea. Recognition of the new subphylum Phoroniformea within the Brachiopoda follows Cohen (2000) [Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.). Proc. R. Soc. Lond. B 267: 225-231]. Classification within the subfamilies Craniiformea, Linguliformea and Rhynchonelliformea is based on the system used in the Treatise on Invertebrate Paleontology Part H Brachiopoda, vol. 2 & 3 (2000), published by the University of Kansas and the Geological Society of America. Information from this publication is presented at: http://www.com.univ-mrs.fr/EuroBrachNet/CLASS/Class.htm
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Mosses

The mosses (Musci) have recently been reorganized according to the classification of Buck and Goffinet (2000), in order to more accurately reflect our current understanding of moss phylogeny. Major features of the new classification include: the elevation of the moss clade to Bryophyta (NOT to be confused with 'bryophytes', referring to a paraphyletic group comprising mosses, liverworts and anthocerotes), and the recognition of three new major clades, Andreaeobryopsida, Takakiopsida and Polytrichopsida, of equal rank with Bryposida, Sphagnopsida, and Andreaeopsida. The 15 suborders of Bryales recognized by Vitt (1984) have been folded, for the most part, into four subclasses of Bryopsida (Bryidae, Dicranidae, Diphysciidae and Funariidae).

References cited:

Buck, W.R. and B. Goffinet. 2000. Morphology and classification of mosses. In Shaw, A.J. and Goffinet, B. (Eds.) The Biology of Bryophytes. Cambridge University Press. In press.

Vitt, D.H. 1984. Classification of the Bryopsida. In R.M. Schuster (Ed.). New Manual of Bryology, vol 2, 266-759. Hattori Botanical Laboratory, Nichinan, Japan.
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Takifugu and Fugu

The pufferfish genus Fugu has been renamed Takifugu in the taxonomy database. This is based on the recommendation of: Matsuura, K. 1990. The pufferfish genus Fugu Abe, 1952, a junior subjective synonym of Takifugu Abe, 1949. Bull. Natn. Sci. Mus., Tokyo, Ser. A. 18(1):15-20. Takifugu includes the species Takifugu rubripes (formerly Fugu rubripes), which is a well known model organism for the vertebrate genome. Any sequence from Takifugu rubripes can still be retrieved by searching on 'Fugu rubripes', because Fugu rubripes is included in the database as a synonym of Takifugu rubripes.
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What are the Euteleostomi?

The name Euteleostomi was recently included in the taxonomy database for the monophyletic group comprising the the Sarcopterygii ('lobe-finned fishes' and tetrapods) plus the Actinopterygii ('ray-finned fishes'). The group was formerly named the 'bony vertebrates' in the database.

Previously, the name Osteichthyes has also been applied to the monophyletic euteleostomes or 'bony vertebrates.' However the name Osteichthyes has been traditionally applied to the 'bony fishes', a paraphyletic assemblage comprising Actinopterygii and Sarcopyterygii minus the tetrapods. For this reason, application of the name Osteichthyes to the monophyletic group of all Sarcopterygii and Actinopterygii was not well accepted. The name Euteleostomi was first proposed as an alternative, to overcome these problems, in:

Nelson, J.S. (1994). p.65, "Fishes of the World," 3rd edition. John Wiley and Sons, New York.
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Sharks and rays

The elasmobranch section (sharks and rays) of the taxonomy database has been revised. The Elasmobranchii is divided into two main clades: the Galeomorphi (comprising the clades Galeoidea and Heterodontidea), and the Squalea (comprising the Dalatioidei, Echinorhinoidea, Hypnosqualea, Notidanoidea and Squaloidei). The Hypnosqualea includes the Squatiniformes, Pristiophoriformes, and the Batoidea which was previously named the Rajiformes (the Rajiformes is currently restricted to the Rajidae [skates]). Batoid interrelationships have been revised, though they remain enigmatic. Thus, the classification and phylogeny presented here is not a definitive one. Nevertheless, it is intended to provide a practical and informative composite of the hypotheses presented in the following most recent overviews of elsamobranch interrelationships:

de Carvalho, M.R. (1996) Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. p.35-62 in: M.L.J. Stiassny, L.R. Parenti, and G.D. Johnson (eds), "Interrelationships of Fishes." Academic Press, San Diego and London.

McEachran, J.D., Dunn, K.A, and Miyake, T. (1996) Interrelationships of the batoid fishes (Chondrichthyes: Batoidea). p.63-84 in: M.L.J. Stiassny, L.R. Parenti, and G.D. Johnson (eds), "Interrelationships of Fishes." Academic Press, San Diego and London.

Shirai, S. (1996) Phylogenetic interrelationships of Neoselachians (Chondrichthyes: Euselachii). p.9-34 in: M.L.J. Stiassny, L.R. Parenti, and G.D. Johnson (eds), "Interrelationships of Fishes." Academic Press, San Diego and London.
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