A transcriptomic analysis of the phylum Nematoda

Parkinson, John; Mitreva, Makedonka; Whitton, Claire; Thomson, Marian; Daub, Jennifer; Martin, John; Schmid, Ralf; Hall, Neil; Barrell, Bart; Waterston, Robert H.; McCarter, James P.; Blaxter, Mark

doi:10.1038/ng1472

Cited by 246 publications

(202 citation statements)

References 41 publications

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“…These ASP-like molecules were also specific for O. ostertagi and T. circumcincta and seem to have diverged early in the evolution of the nematode ASPs. These observations are in agreement with the results from Parkinson et al (2004) who showed that genes containing the SCP/Tpx-1/Ag5/PR-1/Sc7 domain have undergone lineage-specific amplification and divergence within the Strongyloidea. The function of ASP molecules in parasitic nematodes is still unclear.…”

Section: Discussionsupporting

confidence: 93%

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Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi

Visser

Zeveren

Meyvis

et al. 2008

International Journal for Parasitology

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Activation associated secreted proteins (ASP) are members of a nematode-specific protein family belonging to the SCP/Tpx-1/Ag5/ PR-1/Sc7 family. Three different types of molecules have been identified in this family: two-domain ASPs and single-domain ASPs showing homology to either the C-terminal or N-terminal domain of the two-domain ASP. The function of these proteins is still unclear, but a role in transition to parasitism and a role as allergen are often suggested. Here we report that the abomasal cattle parasite Ostertagia ostertagi produces at least 15 ASPs, including two-domain and C-and N-type single-domain ASPs. Ten of these are highly transcribed in the L4 stage, whereas others are highly enriched in adult male worms. The latter was especially the case for the N-type single-domain ASPs Oo-ASP1 and Oo-ASP2 and also for Oo-ASP3, which is homologous with the Haemonchus contortus and Ancylostoma caninum Ctype single-domain ASPs. Immunohistochemistry showed that Oo-ASP3 was localised in the oesophagus. Oo-ASP1 and Oo-ASP2 on the other hand were localised in the reproductive tract of both male and female worms, suggesting a role in reproduction or in the development of the reproductive tract. Ó

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Section: Discussionsupporting

confidence: 93%

“…The ASP protein family seems to be one of the largest nematode-specific protein families (Parkinson et al, 2004). In C. elegans, 36 ASP-like sequences have been found, 23 of them showing significant homology to the Ostertagia ASPs (WORMBASE).…”

Section: Discussionmentioning

confidence: 99%

Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi

Visser

Zeveren

Meyvis

et al. 2008

International Journal for Parasitology

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“…Organization of its mitochondrial genome more closely resembles that of coelomate metazoans than that of its presumed closest relatives, the secernentean nematodes (1). In addition, T. spiralis (Dorylaimia) shares a similar proportion (45%) of its ESTs with the nematode Caenorhabditis elegans (Rhabditina) as it does with the fruit fly Drosophila melanogaster (Arthropoda: Drosophilidae) (2). Thus, many ESTs common to T. spiralis and C. elegans are not necessarily specific to nematodes but may be conserved among diverse taxonomic groups of invertebrates.…”

mentioning

confidence: 99%

Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella

Zarlenga

Rosenthal

Rosa

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

145

124

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Parasitic nematodes of the genus Trichinella cause significant food-borne illness and occupy a unique evolutionary position at the base of the phylum Nematoda, unlike the free-living nematode Caenorhabditis elegans. Although the forthcoming genome sequence of Trichinella spiralis can provide invaluable comparative information about nematode biology, a basic framework for understanding the history of the genus Trichinella is needed to maximize its utility. We therefore developed the first robust and comprehensive analysis of the phylogeny and biogeographic history of Trichinella using the variation in three genes (nuclear small-subunit rDNA, and second internal transcribed spacer, mitochondrial large-subunit rDNA, and cytochrome oxidase I DNA) from all 11 recognized taxa. We conclude that (i) although Trichinellidae may have diverged from their closest extant relatives during the Paleozoic, all contemporary species of Trichinella diversified within the last 20 million years through geographic colonization and pervasive host switching among foraging guilds of obligate carnivores; (ii) mammalian carnivores disseminated encapsulated forms from Eurasia to Africa during the late Miocene and Pliocene, and to the Nearctic across the Bering Land Bridge during the Pliocene and Pleistocene, when crown species ultimately diversified; (iii) the greatest risk to human health is posed by those species retaining an ancestral capacity to parasitize a wide range of hosts; and (iv) early hominids may have first acquired Trichinella on the African savannah several million years before swine domestication as their diets shifted from herbivory to facultative carnivory.biogeography ͉ mitochondrial DNA ͉ phylogeny ͉ ribosomal DNA E xceptional biological diversity among nematodes is exemplified by certain attributes of the parasite Trichinella spiralis. Organization of its mitochondrial genome more closely resembles that of coelomate metazoans than that of its presumed closest relatives, the secernentean nematodes (1). In addition, T. spiralis (Dorylaimia) shares a similar proportion (45%) of its ESTs with the nematode Caenorhabditis elegans (Rhabditina) as it does with the fruit fly Drosophila melanogaster (Arthropoda: Drosophilidae) (2). Thus, many ESTs common to T. spiralis and C. elegans are not necessarily specific to nematodes but may be conserved among diverse taxonomic groups of invertebrates. C. elegans is often thought of as a prototypical nematode because of its acceptance as a model for studying biological processes; however, genomic variation among nematodes is extensive and commensurate with their phylogenetic and ecological diversity. Therefore, the forthcoming genome sequence of T. spiralis will contribute substantially to our understanding of nematode biology and the origins of parasitism.In 1998, Blaxter et al. (3) used genetic data to delineate the phylum Nematoda into supertaxa consisting of five clades. Trichinella, a parasite of vertebrates, occupies a basal lineage (clade I) consisting of free-living Mononchida, ...

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“…For the B. xylophilus data set, the 672 contigs with taxonomy classification were further annotated, with seven assigned to bacteria and 665 assigned to eukaryota (Table 5). (Parkinson et al, 2004;Lilley et al, 2005).…”

Section: Taxonomic Classificationmentioning

confidence: 99%

Expressed sequence tags (EST) analysis of a normalized full-length cDNA library from the pinewood nematode (Bursaphelenchus xylophilus)

Ha¹,

Kang²,

Hye³

et al. 2014

Afr. J. Biotechnol.

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The pinewood nematode (Bursaphelenchus xylophilus) infects pine trees and causes pine wilt disease. To clarify the functions and subcellular localization of B. xylophilus genes/proteins transcribed and predicted from mixed stages (egg, J1, J2, J3 J4 and adult), we prepared a normalized full-length B. xylophilus cDNA library and analyzed expressed sequence tags (ESTs) using the Pendant-Pro sequence analysis suite. Most cDNAs inserted into the library ranged from 0.9 to 1.8 kb (average 1.5 kb). The 1,902 ESTs from B. xylophilus consisted of 286 clusters and 1,273 singletons. EST sizes ranged from 9 to 743 bp with a mean of 336 bp. The predicted protein length from B. xylophilus ESTs revealed that most proteins ranged from 50 to 149 amino acids. Enzyme nomenclature (EC) numbers were classified into 133 (8.5%) of 1,559 contigs using UniProt database hits by the EC numbers method. Transmembrane regions of 1559 clusters were predicted using the TMpred algorithm. The 1,559 contigs with transmembrane regions were annotated; 481 (30.8%) contigs were assigned 'above one' domain and 1,078 (69.1%) were assigned 'none.' Additionally, taxonomy was classified for 672 (43.1%) of 1,559 contigs. Of the 1,559 contigs, 685 (43.9%) were assigned gene ontology terms using the gomerger method of contigs, including singletons. Thirty-one (31) contigs of predicted proteins grouped by BLASTP identity values had significant homology to genes expressed in subcellular structures (for example, mitochondrion, plasma membrane, endoplasmic reticulum, nucleus and golgi). B. xylophilus ESTs provide the foundation for research information on related plant parasite nematodes and contribute to finding an important novel parasite control strategy.

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A transcriptomic analysis of the phylum Nematoda

Cited by 246 publications

References 41 publications

Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi

Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi

Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella

Expressed sequence tags (EST) analysis of a normalized full-length cDNA library from the pinewood nematode (Bursaphelenchus xylophilus)

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