Nematode Tissue Transcriptomes
We take advantage of the size of the large roundworm Ascaris suum and the
ability to physically dissect its separate tissues to study their gene
expression by producing a wide-scale tissue-specific nematode RNA-seq
datasets, including data on three non-reproductive tissues (head, pharynx,
and intestine) in both male and female worms, as well as four reproductive
tissues (testis, seminal vesicle, ovary, and uterus). With this approach
we obtain fundamental information about the biology of diverse cell types
and potential interactions among tissues within this multicellular
organism.
Our studies furthermore focus on the nematode intestine. The intestine is
one of the major organs in nematodes and it creates a key surface
interface with the environment. While specific cellular characteristics
can be diverse among nematode species, intestinal cells typically conform
to polarized epithelial cells with an apical membrane composed of
microvilli lining the digestive tube. This microvillous membrane is
expected to confer an enormous capacity for nutrient digestion and
absorption in nematodes. Furthermore, the intestine is expected to offer
innate immunity against invasive pathogens. For parasitic nematodes,
intestinal adaptations may be required to survive in context of the host
immune systems with which the apical intestinal membrane interfaces. In
addition, the nematode intestine has been suggested to be involved in
other cellular process such as stress response, body size control, aging,
etc. Previous studies have indicated that nematode intestine may be a
prime target for parasite control.
In particular, we focus on i) providing a comprehensive understanding of
genes that are expressed in the adult nematode intestine from parasites
that span the evolutionary extremes of the phylum. The intestinal
transcriptomes from the selected core species are used to determine the
pan-Nematoda intestinal transcriptome. ii) applying advanced bioinformatic
approaches to delineate intestinal genes from all other available nematode
genomes, emphasizing human pathogens that are too small to support direct
analysis of intestinal functions. Intestinal protein families will be
investigated to identify those that have undergone births or deaths and
expansions or contractions throughout nematode evolution. iii) determining
functional categories of intestinal protein families that reflect
adaptable traits of the highest importance in evolution of parasitism.
The distinction of intestinal gene repertoires by clade and species may
reflect the substantial differences in diet and metabolic requirements of
different nematodes, especially parasites. Our studies therefore
contribute to a better understanding of nematode biology and lay
foundations for the development of novel and more effective parasite
controls.
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Publication: Rosa BA, Jasmer DP, Mitreva M. (2014) Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum PLoS Negl Trop Dis. Feb 6;8(2) |
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Publication: Wang Z, Gao X, Martin J, Yin Y, Abubucker S, Rash AC, Li BW, Nash B, Hallsworth-Pepin K, Jasmer DP, Mitreva M. (2013) Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues. Mol Genet Genomics. Jun;288(5-6) |
Data: Active module files for A.suum microarray data by cytoscape
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Publication: Yin,Y., Martin,J., Abubuck,S., Scott,A.L., McCarter,J.P.,Wilson,R.K., Jasmer,D.P., Mitreva,M. (2008) Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus with the Free-living Caenorhabditis elegans. PLoS Neglected Tropical Diseases 2(8) e269. |
Data: Complete KEGG Mappings in Microsoft Excel
Cufflinks transcript assembly (fasta file)
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GO Associations of intestinal genes:
Ascaris suum Intestinal Genes (3,121) |
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Haemonchus contortus Intestinal Genes (1,755) |
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Caenorhabditis elegans Intestinal Genes (5,065) |
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The Core IntFam-241 Protein Families (2,024) |
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