Nomenclature of plant parasitic nematodes

1. Curation and supervision
 An accepted system of gene nomenclature was established for the nematode Caenorhabditis elegans in
the nineteen seventies.
 This system has been refined and consistently used by the many laboratories engaged in active C.
elegans research.
 Increasing amounts of genomic and genetic information have become available for other nematode
species.
 Draft complete genome sequences have been generated for several of these other nematodes, some of
which are being curated by WormBase.
 For these organisms, gene naming will also be supervised by WormBase, in order to maximize
consistency with C. elegans
 It is recommended that nomenclature in general should follow the principles used for C. elegans, as far
as possible.

2. How to Register a New Gene Class or Gene Name
Species Prefixes
 To unambiguously specify the nematode species-of-origin, a 3-letter standard prefix and
hyphen can be added to the gene name
 Prefixes so far used include:
 Cel- = Caenorhabditis elegans
 Cbr- = Caenorhabditis briggsae
 Cbn- = Caenorhabditis brenneri
 Cjp- = Caenorhabditis japonica
 Hba- = Heterorhabditis bacteriophora
 Oti- = Oscheius tipulae
 Ppa- = Pristionchus pacificus
 Cre- = Caenorhabditis remanei

3. Gene naming: Homologous Genes
 Genes predicted from whole genome sequences in other nematode species will, in most
cases, have identifiable close homologs in C. elegans, for which approved names
already exist. In these cases, the same name should be used as in C. elegans, with the
relevant species identifier.
Possible Scenarios
 One-to-one: Where one gene in C. elegans corresponds to a single gene in another
nematode species, ortholog naming can be applied automatically. e.g. thoc-1 in C.
elegans has a C. briggsae ortholog, Cbr-thoc-1.
 One-to-many: Where one gene in C. elegans is related to multiple genes (paralogs) in
another nematode species, these paralogs can be named using additional decimal
numbers. e.g. thoc-3 in C. elegans has two C. briggsae paralogs, Cbr-thoc-3.1 and Cbr-
thoc-3.2.

4. Gene naming cont….
 Many-to-one: Where multiple genes exist in C. elegans, but only a single gene in
another nematode species, either the most closely similar, or the lowest numbered
C. elegans gene, be used to name the single gene, as appropriate
 Many-to-many: Where multiple closely related genes can be identified in both
species, but the phylogenetic relationships of the two sets are complex, new gene
numbers can be assigned to the set of genes in the other nematode species, after
consultation with genenames@wormbase.org.
 In cases where a standard gene name has not yet been assigned in C. elegans, the
gene can be referred to using the cosmid.number identifier for the C. elegans
gene, preceded by a species prefix. e.g. the ortholog of C. elegans W01B11.3 in
Heterorhabditis bacteriophora can be referred to as Hba-W01B11.3. However, in
such cases it will usually be both feasible and desirable to assign a standard name
to the C. elegans gene as well, at the same time.

5. Gene naming cont….
Non-homologous Genes
 It is expected that many genes in other nematode species will lack obvious close
homologs in C. elegans, because of loss or substantial divergence during the
evolution of C. elegans.
 These genes can be given new gene numbers, if they belong to an identifiable
named class in C. elegans, or else new gene name classes can be established for
them.
 In either case, assignment of an approved name should be made after consultation
with genenames@wormbase.org.

6. Gene naming
Forward Genetics
 A significant amount of mutation-based forward genetic analysis is being pursued in
nematodes other than C. elegans, in particular using other species of Caenorhabditis (C.
briggsae, C. remanei, C. brenneri and others), as well as species of Oscheius and
Pristionchus.
 It is expected that most, but not all, of the mutationally-defined genes discovered in these
species will prove to have orthologs with equivalent or similar function in C. elegans,
and hence that standard genetic names will have been approved already. Several
situations can arise:

7. Forward Genetics
1. where the molecular identity is known and orthology is obvious, it is recommended that
the C. elegans name be used, with the appropriate species identifier prefix. e.g. Ppa-mab-5
is the Pristionchus pacificus ortholog of C. elegans mab-5.
2. In cases where the molecular identity is not initially known, but the mutant phenotype
corresponds to a known C. elegans mutant phenotype, it is recommended that the mutant
gene be temporarily defined using the relevant gene class name and the mutation number, in
parentheses. e.g. mutation s1270 isolated in C. briggsae confers an uncoordinated
phenotype, so the gene is temporarily called unc(s1270) or Cbr-unc(s1270).
 Once the molecular identity becomes known, the gene can be given an approved unc-
number, using the number of the C. elegans ortholog (if this exists) or a new number (if
there is no suitable C. elegans ortholog).

8. Forward Genetics
 In cases where the molecular identity is unknown and the mutant phenotype does
not correspond to a known C. elegans mutant phenotype, a new gene class name
can be established, following consultation with genenames@wormbase.org in
order to ensure that the new name is available and appropriate. e.g. cov =
Competence and/or centering Of Vulva abnormal.

9. SPECIFIC NAMES DERIVED FROM HOST NAMES
A parasite named after its hosts should be given the specific (not the
generic) name of its host; this name should be treated as a substantive in
the genitive case.
For example, Hemicaloosia americana is a species from India named
after its host : Agave americana. H. americana is to be spelled H.
amencanae.
Many authors use the generic name of the host. It would not serve the
stability of nomenclature to change these names and they will be
accepted as proposed.

10. SPECIFIC NAMES DERIVED FROM
GEOGRAPHICAL NAMES
 Nothocriconema sanctus-francisci van den Berg & Heyns, 1977, must be
corrected by deletion of a hyphen (Art. 26), and should be written in the
genitive case as N. sanctifrancisci.
 Scutellonema imphalus Sultan & Jairajpuri, 1979, from the town of Imphal,
India, is treated as an adjective. It should be spelled S. imphalum

11. SPECIFIC NAMES FORMED FROM MODERN PERSONAL NAMES
 Aphelenchoides franklini Singh, 1969, from the name of Dr Mary Franklin, is corrected
to A. franklinae. Cosaglenchus rafiqus Siddiqui & Khan, 1983 is corrected to C. rafiqi
(Recommendation 31 A; see also D Ill).
ERRORS IN TARJAN AND HOPPER'S BOOK
 The specific names listed in Tarjan and Hopper (1974) are sometimes spelled with an
ending different from that in the original publication. These discrepancies occurred when
a taxon is better known in a genus different from the original genus, and with a different
gender.
 For example the species named Tylenchus balsamophilus Throne, 1926, in the original
description was spelled T. balsamophila in Tarjan and Hopper's book, probably because
it is now Anguina balsamophila. In the computerized datafile, the spelling has been
reverted to that of the original author,

12. ERRORS IN TARJAN AND HOPPER'S BOOK
 Other typographical errors in Tarjan and Hoppe(1974) include
Anguillonema erenati for A. crenati.
Aphelenchoides eradicatus for A. eradicitus
 These incorrect subsequent spellings have no status in nomenclature (Art. 33, b).
 Another incorrect subsequent spelling was made when Bajaj and Bhatti (1979)
transferred Basiroides longimatricalis Kazachenko, 1975 to Basiria under the
specific name Basiria leptolongimatricalis. The correct new combination is
Basiria longimatricalis (Kazachenko) Bajaj & Bhatti.

13. Common Names of Major Phytonematodes of
Horticultural Crops
 Anguina spp.: Seed and leaf gall
nematode
 A. agrostis : Bent grass
nematode
 Aphelenchoides spp.: Bud and
leaf nematode, foliar nematode
 A. besseyi : Rice white-tip
nematode, strawberry bud
nematode, summer crimp,
summer dwarf nematode
 A. fragariae : Spring crimp
nematode, spring dwarf
nematode, strawberry bud
nematode
 A. ritzemabosi :
Chrysanthemum foliar
nematode
 Bursaphelenchus cocophilus :
Coconut palm nematode, red ring
nematode
 Bursaphelenchus xylophilus :
Pinewood nematode
 Cacopaurus pestis : Walnut nematode
 C. cacti : Cactus cyst nematode
 Criconema / Criconemoides : Ring
nematode
 Ditylenchus destructor : Potato rot
nematode
 D. dipsaci : Stem and bulb nematode,
alfalfa stem nematode
 Dolichodorus spp.: Awl nematode
 Globodera pallida : Pale/white
potato cyst nematode
 G. rostochiensis : Golden nematode,
golden potato cyst nematode

14. Cont….
 Helicotylenchus multicinctus :
Banana spiral nematode, spiral
nematode
 Hemicriconemoides spp.: False
sheath nematode
 Hemicycliophora spp.: Sheath
nematode
 Heterodera carotae : Carrot cyst
nematode
 H. cruciferae : Cabbage cyst
nematode
 H. cyperi : Nutgrass cyst nematode
 H. fici : Fig cyst nematode
 H. goettingiana : Pea cyst nematode
 H. schachtii : Sugar beet cyst
nematode
 Hoplolaimus spp.: Lance nematode
 Longidorus spp.: Needle nematode
 Meloidodera spp.: Cystoid nematode
 Meloidogyne spp.: Root-knot nematode
 M. carolinensis : Blueberry root-knot
nematode
 M. exigua : Coffee root-knot nematode
 M. graminis : Grass root-knot nematode
 M. hapla : Northern root-knot nematode
 M. incognita : Southern root-knot
nematode
 M. javanica : Javanese root-knot
nematode
 M. konaensis : Kona coffee root-knot
nematode
 M. lusitanica : Olive root-knot nematode
 M. megatyla : Pine root-knot nematode
 M. nataliei : Michigan grape root-knot
nematode

15. Cont….
 M. pini : Sand pine root-knot nematode
 Nacobbus spp.: False root-knot
nematode
 Paratrichodorus spp.: Stubby-root
nematode
 Paralongidorus spp.: Needle nematode
 Paratylenchus spp.: Pin nematode
 Pratylenchoides spp.: False-burrowing
nematode
 Pratylenchus spp.: Lesion nematode
 P. coffeae : Coffee lesion nematode
 P. penetrans : Meadow nematode
 P. vulnus : Boxwood lesion nematode,
walnut lesion nematode
 Punctodera punctata : Grass cyst
nematode
 Rodopholous similis : Banana
burrowing nematode, burrowing
nematode
 Rotylenchulus reniformis :
Reniform nematode
 Rotylenchus spp.: Spiral nematode
 Scutellonema bradys : Yam
nematode
 Subanguina radicicola : Grass root-
gall nematode
 Trichodorus spp.: Stubby-root
nematode
 Tylenchorhynchus spp.: Stunt
nematodes
 Tylenchulus semipenetrans : Citrus
nematode
 Xiphinema spp.: Dagger nematode
 X. americanum : American dagger
nematode