NEMBASE4 data summary - numbers and sources

NEMBASE4 identifier	Species	Clade	Life habit	Number of ESTs	Number of cDNA libraries	Number of NEMBASE4 clusters	References
ABC	Ancylostoma braziliense	V	vgp	19	1	18	(Costa et al., 2008)
ACC	Ancylostoma caninum	V	vgp	78935	15	25911	a
AYC	Ancylostoma ceylanicum	V	vgp	10551	9	3489	a
AAC	Angiostrongylus cantonensis	V	vgp	1191	4	650	(He et al., 2009)
AIC	Anisakis simplex	III	vtp	473	1	320	b
ALC	Ascaris lumbricoides	III	vgp	1822	1	853	(Wasmuth et al., 2008)
ASC	Ascaris suum	III	vgp	55343	38	13284	(Wasmuth et al., 2008)
BMC	Brugia malayi	III	vtp	25844	25	9822	(Blaxter et al., 1996; Blaxter et al., 2002; Li et al., 2009)}
BPC	Brugia pahangi	III	vtp	28	2	28	(Emes et al., 2002)
BUC	Bursaphelenchus mucronatus	IV	pep	3191	1	2264	(Kikuchi et al., 2007)
BXC	Bursaphelenchus xylophilus	IV	pep	13338	6	6660	(Kikuchi et al., 2007)
CBC	Caenorhabditis brenneri	V	fl	29443	3	10045	a
CGC	Caenorhabditis briggsae	V	fl*	2406	1	1450	(Stein et al., 2003)
CJC	Caenorhabditis japonica	V	fl*	31598	0	8970	a
CRC	Caenorhabditis remanei	V	fl	20166	2	9148	a
CSC	Caenorhabditis sp_5_AC-2008	V	fl	3866	1	2245	c
DVC	Dictyocaulus viviparus	IV	vlp	4423	3	2433	(Ranganathan et al., 2007)
DIC	Dirofilaria immitis	III	vtp	3762	2	1783	(Yin et al., 2006)
DAC	Ditylenchus africanus	IV	pxp	4289	1	2513	a
GMC	Globodera mexicana	IV	pep	17	1	17	(Grenier et al., 2002)
GPC	Globodera pallida	IV	pep	3900	4	2564	(Jones et al., 2009)
GRC	Globodera rostochiensis	IV	pep	11658	6	4540	a
HCC	Haemonchus contortus	V	vgp	22257	14	4972	(Wasmuth et al., 2008)
HGC	Heterodera glycines	IV	pep	24167	14	9174	a, d
HSC	Heterodera schachtii	IV	pep	2791	3	1371	a
HBC	Heterorhabditis bacteriophora	V	epn	42354	8	10483	a
LSC	Litomosoides sigmodontis	III	vtp	2699	3	1631	(Allen et al., 2000)
LLC	Loa loa	III	vtp	27	1	26	e
MAC	Meloidogyne arenaria	IV	pep	4979	5	2623	f
MCC	Meloidogyne chitwoodi	IV	pep	11938	4	3793	a
MHC	Meloidogyne hapla	IV	pep	23992	6	6946	a
MIC	Meloidogyne incognita	IV	pep	19806	11	5985	(Dubreuil et al., 2007)
MJC	Meloidogyne javanica	IV	pep	7275	8	3369	a
MPC	Meloidogyne paranaensis	IV	pep	3638	2	1636	a
NAC	Necator americanus	V	vgp	5019	4	2446	(Rabelo et al., 2009)
NBC	Nippostrongylus brasiliensis	V	vgp	13673	8	3569	(Harcus et al., 2004) and *
ODC	Oesophagostomum dentatum	V	vgp	299	2	249	(Cottee et al., 2006)
OFC	Onchocerca flexuosa	III	vtp	2063	2	1525	a
OCC	Onchocerca ochengi	III	vtp	59	1	37	g
OVC	Onchocerca volvulus	III	vtp	14791	10	5105	(Lizotte-Waniewski et al., 2000; Pellerone et al., 2003)
OOC	Ostertagia ostertagi	V	vgp	6761	10	2367	(Vercauteren et al., 2003)
PSC	Panagrolaimus superbus	IV	fl	7606	0	3957	h
PTC	Parastrongyloides trichosuri	IV	vgp*	7776	6	3128	a
PAC	Parelaphostrongylus tenuis	V	vgp	99	1	95	i
PEC	Pratylenchus penetrans	IV	pep	1919	1	410	a
PVC	Pratylenchus vulnus	IV	pep	5762	3	1824	a
PPC	Pristionchus pacificus	V	fl	35736	11	10577	(Srinivasan et al., 2004)
RSC	Radopholus similis	IV	pep	7164	5	3871	(Jacob et al., 2008) and j
SCC	Steinernema carpocapsae	IV	epn	44	1	43	(Hao et al., 2010)
SFC	Steinernema feltiae	IV	epn	83	1	74	(Gal et al., 2003)
SRC	Strongyloides ratti	IV	vgp*	26400	12	5058	(Evans et al., 2008)
SSC	Strongyloides stercoralis	IV	vgp*	11365	3	3681	a
TDC	Teladorsagia circumcincta	V	vgp	6011	5	2262	(Parkinson et al., 2004; Nisbet et al., 2008)
TLC	Toxascaris leonina	III	vgp	434	1	279	k
TCC	Toxocara canis	III	vgp**	4791	6	1537	(Parkinson et al., 2004; Callister et al., 2008) and l
TSC	Trichinella spiralis	I	vgp**	24678	8	8509	a
TIC	Trichostrongylus vitrinus	V	vgp	367	2	359	(Nisbet and Gasser, 2004)
TMC	Trichuris muris	I	vgp	6891	3	3037	a
TVC	Trichuris vulpis	I	vgp	2959	1	1258	a
WBC	Wuchereria bancrofti	III	vtp	4871	3	2222	a
XIC	Xiphinema index	I	pxp	9283	7	4591	a
ZPC	Zeldia punctata	IV	fl	390	1	209	a
Total	62 species			679480	324	233295

Clade: Nematode clades are as defined in Blaxter et al 1998 (Blaxter et al., 1998) (see also (Meldal et al., 2007)). I: Dorylaimia, including Dorylaimida and Trichocephalida; III: Spiruria, including Spiruromorpha and Ascaridida; IV: Tylenchia, including Cephalobomorpha, Strongyloidoiea, and Tylenchida; V: Rhabditia, including Rhabditida, Strongylida, and Diplogasterida. There are no Clade II (Enoplia) expressed sequence tag (EST) datasets at present.
Life habit: epn: entomopathogenic nematode; fl: free-living; fl* free-living, but associated with arthropod transport hosts; pxp: plant exoparasite; vgp: vertebrate gut parasite; vgp*: vertebrate gut parasite with free-living cycle(s); vgp**: vertebrate gut parasite with intracellular resting stage; vtp: vertebrate tissue parasite.

a No specific publication associated with this dataset; data produced by Washington University of St. Louis Genome Sequencing Center (see Wasmuth et al., 2008))
b No specific publication associated with this dataset; data produced by College of Medicine, Pusan University, Korea.
c Asher Cutter and Mark Blaxter, unpublished data.
d Some data produced by National Agricultural Research Center for Hokkaido Region, Sapporo, Hokkaido 062-8555, Japan.
e No specific publication associated with this dataset; data produced by Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIAID, NIH, USA.
f No specific publication associated with this dataset; data produced by College of Plant Protection, Nanjing Agricultural University, Weigang, Nanjing, China.
g No specific publication associated with this dataset; data produced by Molecular Parasitology, Department of Biological Sciences, Smith College, Northampton, USA.
h Ann Burnell and colleagues, UI Maynooth, unpublished data.
i No specific publication associated with this dataset; data produced by James A. Baker Institute, Cornell University, Ithaca, NY, USA
j No specific publication associated with this dataset; data produced by Department of Plant Pathology, College of Natural Resources and Environment, South China Agricultural University, Guangdong, China.
k No specific publication associated with this dataset; data produced by Department of Parasitology, Pusan National University, School of Medicine, Seo-gu, Busan, Korea.
l No specific publication associated with this dataset; data produced by Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing Municipality, China

References

Allen, J.E., Daub, J., Guiliano, D., McDonnell, A., Lizotte-Waniewski, M., Taylor, D.W., Blaxter, M., 2000. Analysis of genes expressed at the infective larval stage validates utility of Litomosoides sigmodontis as a murine model for filarial vaccine development. Infect Immun 68, 5454-5458.
Blaxter, M., Daub, J., Guiliano, D., Parkinson, J., Whitton, C., 2002. The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans R Soc Trop Med Hyg 96, 7-17.
Blaxter, M.L., Raghavan, N., Ghosh, I., Guiliano, D., Lu, W., Williams, S.A., Slatko, B., Scott, A.L., 1996. Genes expressed in Brugia malayi infective third stage larvae. Molecular and Biochemical Parasitology 77, 77-96.
Blaxter, M.L., De Ley, P., Garey, J.R., Liu, L.X., Scheldeman, P., Vierstraete, A., Vanfleteren, J.R., Mackey, L.Y., Dorris, M., Frisse, L.M., Vida, J.T., Thomas, W.K., 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392, 71-75.
Callister, D.M., Winter, A.D., Page, A.P., Maizels, R.M., 2008. Four abundant novel transcript genes from Toxocara canis with unrelated coding sequences share untranslated region tracts implicated in the control of gene expression. Mol Biochem Parasitol 162, 60-70.
Costa, A.F., Gomes-Ruiz, A.C., Rabelo, E.M., 2008. Identification of gender-regulated genes in Ancylostoma braziliense by real-time RT-PCR. Vet Parasitol 153, 277-284.
Cottee, P.A., Nisbet, A.J., Abs El-Osta, Y.G., Webster, T.L., Gasser, R.B., 2006. Construction of gender-enriched cDNA archives for adult Oesophagostomum dentatum by suppressive-subtractive hybridization and a microarray analysis of expressed sequence tags. Parasitology 132, 691-708.
Dubreuil, G., Magliano, M., Deleury, E., Abad, P., Rosso, M.N., 2007. Transcriptome analysis of root-knot nematode functions induced in the early stages of parasitism. New Phytol 176, 426-436.
Emes, R., Thompson, F., Moore, J., Zang, X., Devaney, E., 2002. Cloning and characterisation of mmc-1, a microfilarial-specific gene, from Brugia pahangi. Int J Parasitol 32, 415-424.
Evans, H., Mello, L.V., Fang, Y., Wit, E., Thompson, F.J., Viney, M.E., Paterson, S., 2008. Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti. Int J Parasitol 38, 1329-1341.
Gal, T.Z., Glazer, I., Koltai, H., 2003. Differential gene expression during desiccation stress in the insect-killing nematode Steinernema feltiae IS-6. J Parasitol 89, 761-766.
Grenier, E., Blok, V.C., Jones, J.T., Fouville, D., Mugniery, D., 2002. Identification of gene expression differences between Globodera pallida and G.'mexicana' by suppression subtractive hybridization. Mol Plant Pathol 3, 217-226.
Hao, Y.J., Montiel, R., Abubucker, S., Mitreva, M., Simoes, N., 2010. Transcripts analysis of the entomopathogenic nematode Steinernema carpocapsae induced in vitro with insect haemolymph. Mol. Biochem. Parasitol. 169, 79-86.
Harcus, Y.M., Parkinson, J., Fernandez, C., Daub, J., Selkirk, M.E., Blaxter, M.L., Maizels, R.M., 2004. Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites. Genome Biol 5, R39.
He, H., Cheng, M., Yang, X., Meng, J., He, A., Zheng, X., Li, Z., Guo, P., Pan, Z., Zhan, X., 2009. Preliminary molecular characterization of the human pathogen Angiostrongylus cantonensis. BMC Mol Biol 10, 97.
Jacob, J., Mitreva, M., Vanholme, B., Gheysen, G., 2008. Exploring the transcriptome of the burrowing nematode Radopholus similis. Mol Genet Genomics 280, 1-17.
Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., Castelli, L., Chapman, S., Cock, P.J., Grenier, E., Lilley, C.J., Phillips, M.S., Blok, V.C., 2009. Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. Mol Plant Pathol 10, 815-828.
Kikuchi, T., Aikawa, T., Kosaka, H., Pritchard, L., Ogura, N., Jones, J.T., 2007. Expressed sequence tag (EST) analysis of the pine wood nematode Bursaphelenchus xylophilus and B. mucronatus. Mol. Biochem. Parasitol. 155, 9-17.
Li, B.W., Rush, A.C., Mitreva, M., Yin, Y., Spiro, D., Ghedin, E., Weil, G.J., 2009. Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3. BMC Genomics 10, 267.
Lizotte-Waniewski, M., Tawe, W., Guiliano, D.B., Lu, W., Liu, J., Williams, S.A., Lustigman, S., 2000. Identification of potential vaccine and drug target candidates by expressed sequence tag analysis and immunoscreening of Onchocerca volvulus larval cDNA libraries. Infect Immun 68, 3491-3501.
Meldal, B.H., Debenham, N.J., De Ley, P., De Ley, I.T., Vanfleteren, J.R., Vierstraete, A.R., Bert, W., Borgonie, G., Moens, T., Tyler, P.A., Austen, M.C., Blaxter, M.L., Rogers, A.D., Lambshead, P.J., 2007. An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa. Mol Phylogenet Evol 42, 622-636.
Nisbet, A.J., Gasser, R.B., 2004. Profiling of gender-specific gene expression for Trichostrongylus vitrinus (Nematoda: Strongylida) by microarray analysis of expressed sequence tag libraries constructed by suppressive-subtractive hybridisation. Int J Parasitol 34, 633-643.
Nisbet, A.J., Redmond, D.L., Matthews, J.B., Watkins, C., Yaga, R., Jones, J.T., Nath, M., Knox, D.P., 2008. Stage-specific gene expression in Teladorsagia circumcincta (Nematoda: Strongylida) infective larvae and early parasitic stages. Int J Parasitol 38, 829-838.
Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R.H., McCarter, J.P., Blaxter, M.L., 2004. A transcriptomic analysis of the phylum Nematoda. Nat Genet 36, 1259-1267.
Pellerone, F.I., Archer, S.K., Behm, C.A., Grant, W.N., Lacey, M.J., Somerville, A.C., 2003. Trehalose metabolism genes in Caenorhabditis elegans and filarial nematodes. Int J Parasitol 33, 1195-1206.
Rabelo, E.M., Hall, R.S., Loukas, A., Cooper, L., Hu, M., Ranganathan, S., Gasser, R.B., 2009. Improved insights into the transcriptomes of the human hookworm Necator americanus--fundamental and biotechnological implications. Biotechnol Adv 27, 122-132.
Ranganathan, S., Nagaraj, S.H., Hu, M., Strube, C., Schnieder, T., Gasser, R.B., 2007. A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus. BMC Genomics 8, 311.
Srinivasan, J., Otto, G.W., Kahlow, U., Geisler, R., Sommer, R.J., 2004. AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus. Nucleic Acids Res 32, D421-422.
Stein, L.D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M.R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, D.H., Fulton, L.A., Fulton, R.E., Griffiths-Jones, S., Harris, T.W., Hillier, L.W., Kamath, R., Kuwabara, P.E., Mardis, E.R., Marra, M.A., Miner, T.L., Minx, P., Mullikin, J.C., Plumb, R.W., Rogers, J., Schein, J.E., Sohrmann, M., Spieth, J., Stajich, J.E., Wei, C., Willey, D., Wilson, R.K., Durbin, R., Waterston, R.H., 2003. The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biol 1, E45.
Vercauteren, I., Geldhof, P., Peelaers, I., Claerebout, E., Berx, G., Vercruysse, J., 2003. Identification of excretory-secretory products of larval and adult Ostertagia ostertagi by immunoscreening of cDNA libraries. Mol Biochem Parasitol 126, 201-208.
Wasmuth, J., Schmid, R., Hedley, A., Blaxter, M., 2008. On the extent and origins of genic novelty in the phylum nematoda. PLoS Negl Trop Dis 2, e258.
Yin, Y., Martin, J., McCarter, J.P., Clifton, S.W., Wilson, R.K., Mitreva, M., 2006. Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis. Int J Parasitol 36, 829-839.