Table 1.
Intestinal Transcriptomes and Intestine-Enriched Genes from Three Nematodes.
Figure 1.
Sequence Similarities Identified in the A. suum and H. contortus Intestinal Transcriptomes.
The three phylogenetically specific sequence groups used to identify sequence similarities of the intestinal genes were: i) Caenorhabditis spp., amino acid sequences from the complete genomes of C. elegans, C. briggsae, and C. remanei, ii) Other Nematoda, non-Caenorhabditis nematode nucleic acid sequences excluding those from either A. suum or H. contortus, when sequences from A. suum or H. contortus were queried, respectively, and iii) Non-Nematoda, non-nematode amino acid sequences from the non-redundant protein database NR. In total, 61% (1,893/3,121) A. suum and 81% (1,423/1,755) H. contortus intestinal genes contained primary sequence similarities to known proteins from other organisms.
Figure 2.
Putative Secreted or Trans-membrane Proteins in A. suum, H. contortus, and C. elegans.
Larger percentages of the putative intestine-enriched genes (Int. Enriched) were predicted to be secreted with signal peptide (SP) or trans-membrane (TM) than either the complete set of intestinal genes (Int. Genes) or the complete set of all available genes (All Genes) in A. suum, H. contortus, and C. elegans.
Figure 3.
Orthologous Genes Tend to Maintain Their Intestinal Expression Patterns across A. suum and C. elegans.
A total of 289 putative orthologous pairs were identified among the intestine or gonad gene groups from A. suum and C. elegans. Ninety such pairs were found between the two intestine gene groups, representing an enrichment of 31% over the expectation from a random distribution of orthologous pairs, and an enrichment of only 5% was detected between genes in the two gonad groups. The null hypothesis of random orthologous pairing was rejected at a confidence level of at least 99% with a χ2 value of 11.9 between the observations and expectations.
Figure 4.
Protein Families in the Adult Intestine from A. suum, H. contortus, and C. elegans.
In total, 5,587 intestinal protein families (IntFam) were built from the complete set of 9,918 translated intestinal genes sampled from the three species. Forty-one percent of all the intestinal genes were grouped into 910 multiple-species IntFam groups; 2,024 genes, including 752 from A. suum, 455 from H. contortus, and 817 from C. elegans, were found in a group of 241 families (IntFam-241) containing members from all three intestines. The IntFam-241 families likely represent an ancestral intestinal transcriptome involved in core cellular and physiological intestinal functions common to the investigated species or even to Nematoda, they are thus referred as the “core” IntFam-241 group.
Table 2.
Gene Ontology Terms Statistically Enriched among 2,024 Intestinal Genes in IntFam-241.
Table 3.
Selected Gene Ontology Annotations in IntFam-241.
Table 4.
KEGG Pathway Mappings for Intestinal Genes from Three Nematodes.
Table 5.
RNA interference (RNAi) Phenotypes Assigned to IntFams through C. elegans Members.