TY - JOUR
T1 - Gene discovery in the adenophorean nematode Trichinella spiralis
T2 - An analysis of transcription from three life cycle stages
AU - Mitreva, Makedonka
AU - Jasmer, Douglas P.
AU - Appleton, Judith
AU - Martin, John
AU - Dante, Mike
AU - Wylie, Todd
AU - Clifton, Sandra W.
AU - Waterston, Robert H.
AU - McCarter, James P.
N1 - Funding Information:
T. spiralis EST sequencing at Washington University was supported by NIH-NIAID research grant AI 46593 to RHW. The authors would like to thank B. Chiapelli, C. Murphy and D. Pape for technical assistance. JPM was supported by a Helen Hay Whitney/Merck Fellowship. JPM is employee and equity holder of Divergence Inc; this research was not company funded.
PY - 2004/10
Y1 - 2004/10
N2 - Expressed sequence tags (ESTs) were produced from cDNA libraries for immature L1, mature muscle larva and adult stages of the adenophorean nematode Trichinella spiralis. 10,130 ESTs were grouped into 3454 gene clusters. The clusters represent a conservative estimate of 3262 unique genes. Interspecific comparisons of the predicted proteins support an ancient divergence of clade I nematodes from other nematodes in the phylum Nematoda. Furthermore, apparent clade I or Trichocephalida-specific proteins were identified, which may include molecular determinants important in the evolution of these species. Similarity matches identified 463 C. elegans genes homologs that confer phenotypes by RNA interference. Classification of predicted proteins suggested diverse cellular, metabolic and extracellular functions, significantly expanding the dataset of T. spiralis proteins with prospective, and potentially critical, functions. Several lines of evidence suggested stage-specific expression of certain genes beyond those previously identified. Evidence was obtained for the existence of large gene families encoding isoforms of known secreted proteins, such as p43 and TspE1. Unexpectedly, diverse isoforms of the muscle larva p43 gene appear to be expressed by immature L1. Proteinases, kinases, antioxidant proteins and enzymes involved in glycan synthesis are implicated in T. spiralis interactions with its hosts. Numerous genes were identified that encode predicted proteins in these categories. The genes discovered, when put into context of functional classification, stage of expression, and biology of the parasite, should substantially enhance experimental potential for research on this parasite.
AB - Expressed sequence tags (ESTs) were produced from cDNA libraries for immature L1, mature muscle larva and adult stages of the adenophorean nematode Trichinella spiralis. 10,130 ESTs were grouped into 3454 gene clusters. The clusters represent a conservative estimate of 3262 unique genes. Interspecific comparisons of the predicted proteins support an ancient divergence of clade I nematodes from other nematodes in the phylum Nematoda. Furthermore, apparent clade I or Trichocephalida-specific proteins were identified, which may include molecular determinants important in the evolution of these species. Similarity matches identified 463 C. elegans genes homologs that confer phenotypes by RNA interference. Classification of predicted proteins suggested diverse cellular, metabolic and extracellular functions, significantly expanding the dataset of T. spiralis proteins with prospective, and potentially critical, functions. Several lines of evidence suggested stage-specific expression of certain genes beyond those previously identified. Evidence was obtained for the existence of large gene families encoding isoforms of known secreted proteins, such as p43 and TspE1. Unexpectedly, diverse isoforms of the muscle larva p43 gene appear to be expressed by immature L1. Proteinases, kinases, antioxidant proteins and enzymes involved in glycan synthesis are implicated in T. spiralis interactions with its hosts. Numerous genes were identified that encode predicted proteins in these categories. The genes discovered, when put into context of functional classification, stage of expression, and biology of the parasite, should substantially enhance experimental potential for research on this parasite.
KW - Comparative genomics
KW - Expressed sequence tags
KW - Gene expression
KW - Nematode
KW - Parasite
KW - Trichinella
UR - http://www.scopus.com/inward/record.url?scp=4644313801&partnerID=8YFLogxK
U2 - 10.1016/j.molbiopara.2004.05.015
DO - 10.1016/j.molbiopara.2004.05.015
M3 - Article
C2 - 15383298
AN - SCOPUS:4644313801
SN - 0166-6851
VL - 137
SP - 277
EP - 291
JO - Molecular and Biochemical Parasitology
JF - Molecular and Biochemical Parasitology
IS - 2
ER -