Comparative genomics : tissue transcriptome

Bioinformatics Workshop for Helminth Genomics (2015) class materials now freely available!

NTDs get some well deserved coverage outside the usual channels: Financial Times Special Report: Neglected Tropical Diseases

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.


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)

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)

Active module files for A.suum microarray data by cytoscape

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.

Complete KEGG Mappings in Microsoft Excel
Cufflinks transcript assembly (fasta file)

GO Associations of intestinal genes:
Ascaris suum Intestinal Genes (3,121)
Haemonchus contortus Intestinal Genes (1,755)
Caenorhabditis elegans Intestinal Genes (5,065)
The Core IntFam-241 Protein Families (2,024) v4.0           Copyright Statement
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