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PubMed2003

Mobile genetic elements colonizing the genomes of metazoan parasites.

A substantial fraction of the genome of most eukaryotes, including those of metazoan parasites, is predicted to comprise repetitive sequences. Mobile genetic elements (MGEs) will make up much of these repetitive sequences, particularly the interspersed sequences. This article reviews information on MGEs that have colonized the genomes of metazoan parasites (i.e. parasites of parasites). Helminth and mosquito genomes, in particular, are compared with those of better-understood model organisms. MGEs from the genomes of metazoan parasites can be expected to have practical uses in transgenesis and epidemiological studies.

Animals↗
PubMed2001

A gene family expressing a host-protective antigen of Echinococcus granulosus.

Echinococcus granulosus causes cystic hydatidosis in humans. A recombinant antigen vaccine has been developed, for use in the parasite's natural animal intermediate hosts, that may provide a new tool for control of hydatid disease transmission. The antigen, designated EG95, is encoded by a cDNA the features of which indicate it to be an incomplete copy of the associated mRNA. Characterisation of the gene(s) encoding the antigen was undertaken in order to enable subsequent study of genetic variability in the gene and associated protein in different parasite isolates. Southern hybridisation studies of E. granulosus genomic DNA probed with the eg95 cDNA revealed that the gene belonged to a gene family. DNA sequence analysis of cloned genomic fragments indicated that the gene family consists of at least seven members, one of which is a pseudogene. The gene having identity with the eg95 cDNA was cloned and sequenced, and the full length mRNA characterised. Genomic sequence and structure of the eg95 gene family members are highly conserved with respect to the gene encoding EG95. Four eg95-related genes are predicted to express an identical EG95 protein and all four were shown to be expressed in the oncosphere life-cycle stage. The full length EG95 protein has a predicted molecular mass of 16.9 kDa, secretory signal sequence, carboxy-terminal glycosylphosphatidylinositol hydrophobic anchor motif and a fibronectin type III domain. PCR amplification conditions were established which allow gene-specific characterisation of the eg95 gene in E. granulosus isolates from different host species and geographical locations.

5' Untranslated Regions↗
PubMed1999

Gene duplication and gene conversion in the Caenorhabditis elegans genome.

A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only 2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative rates of duplication and deletion may contribute to the compactness of the C. elegans genome.

Animals↗
PubMed1997

Genome sizes of the entomopathogenic nematodes Steinernema carpocapsae and Heterorhabditis bacteriophora (Nematoda:Rhabditida).

There is currently no information on the genome size and complexity in the entomoparasitic nematodes Steinernema and Heterorhabditis. DNA reassociation kinetics were used to determine the genome size and complexity in 2 species: Steinernema carpocapsae and Heterorhabditis bacteriophora. C0t curves derived from renaturation kinetics of denatured DNA indicate that the genomes of these entomoparasitic rhabditids are different both in size and complexity. Genome sizes were estimated at 2.3 x 10(8) bp for S. carpocapsae and 3.9 x 10(7) bp for H. bacteriophora and repetitive DNA contents were found to represent 39% and 51% of these respective genomes.

Animals↗
PubMed2001

Cloning and characterization of SmZF1, a gene encoding a Schistosoma mansoni zinc finger protein.

The zinc finger motifs (Cys2His2) are found in several proteins playing a role in the regulation of transcripton. SmZF1, a Schistosoma mansoni gene encoding a zinc finger protein was initially isolated from an adult worm cDNA library, as a partial cDNA. The full sequence of the gene was obtained by subcloning and sequencing cDNA and genomic fragments. The collated gene sequence is 2181 nt and the complete cDNA sequence is 705 bp containing the full open reading frame of the gene. Analysis of the genome sequence revealed the presence of three introns interrupting the coding region. The open reading frame theoretically encodes a protein of 164 amino acids, with a calculated molecular mass of 18,667Da. The predicted protein contains three zinc finger motifs, usually present in transcription regulatory proteins. PCR amplification with specific primers for the gene allowed for the detection of the target in egg, cercariae, schistosomulum and adult worm cDNA libraries indicating the expression of the mRNA in these life cycle stages of S. mansoni. This pattern of expression suggests the gene plays a role in vital functions of different life cycle stages of the parasite. Future research will be directed to elucidate the functional role of SmZF1.

Animals↗
PubMed1997

end-1 encodes an apparent GATA factor that specifies the endoderm precursor in Caenorhabditis elegans embryos.

The endoderm in the nematode Caenorhabditis elegans is clonally derived from the E founder cell. We identified a single genomic region (the endoderm-determining region, or EDR) that is required for the production of the entire C. elegans endoderm. In embryos lacking the EDR, the E cell gives rise to ectoderm and mesoderm instead of endoderm and appears to adopt the fate of its cousin, the C founder cell. end-1, a gene from the EDR, restores endoderm production in EDR deficiency homozygotes. end-1 transcripts are first detectable specifically in the E cell, consistent with a direct role for end-1 in endoderm development. The END-1 protein is an apparent zinc finger-containing GATA transcription factor. As GATA factors have been implicated in endoderm development in other animals, our findings suggest that endoderm may be specified by molecularly conserved mechanisms in triploblastic animals. We propose that end-1, the first zygotic gene known to be involved in the specification of germ layer and founder cell identity in C. elegans, may link maternal genes that regulate the establishment of the endoderm to downstream genes responsible for endoderm differentiation.

Amino Acid Sequence↗
PubMed1997

cut-1-like genes of Ascaris lumbricoides.

Three genomic fragments homologous to cut-1 of Caenorhabditis elegans (C. elegans) have been identified in the intestinal parasitic nematode Ascaris lumbricoides (A. lumbricoides). Two of these fragments identify one region of the A. lumbricoides genome; they are separated by 8-9 kb and have opposite orientation, with the direction of transcription converging toward the center of the region. The third gene, which has been studied more completely, is in a different region of the genome separated from the first one by not less than 12-15 kb. The complete genomic sequence of this third gene has been determined. cDNA overlapping clones were obtained from adult A. lumbricoides RNA via the rapid amplification of cDNA ends (RACE) procedure [Frohman et al., 1988. Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85, 8998-9002] and sequenced. The mature mRNA of this gene, which we have named ascut-1, is trans-spliced to the spliced leader sequence of nematodes (SL1) [Krause, M., Hirsh, D., 1987. A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49, 753-761]. The mRNA is 1684 nt long plus the poly(A) tail and contains four exons with a 138 nt untranslated 5' leader and a 388 nt untranslated 3' tail. Conceptual translation of the coding sequence shows a protein of 385 aa with a signal peptide of 16 aa. The protein shows very high homology with CECUT-1, the product of the C. elegans gene cut-1 and with other cuticlin proteins of nematodes. A 262 amino acids region which is strongly conserved between these proteins seems to identify a group of proteins, so far restricted to nematodes, for which the name CUT-1-like is proposed.

Amino Acid Sequence↗
PubMed2001

Broadcast interference - functional genomics.

Four recent papers mark a major shift in functional genomic analysis for multicellular organisms. RNA-mediated interference was applied to inactivate individual genes systematically on a genomic scale. These studies subjected a third of the genes in the genome of Caenorhabditis elegans to reverse genetic analysis.

Animals↗
PubMed2024

Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing.

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the C. elegans reference and 99.5% of the annotated C. elegans reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic C. elegans genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains.

Caenorhabditis elegans↗
PubMed2000

The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses.

The srh family of chemoreceptors in the nematode Caenorhabditis elegans is very large, containing 214 genes and 90 pseudogenes. It is related to the str, stl, and srd families of seven-transmembrane or serpentine receptors. Like these three families, most srh genes are concentrated on chromosome V, and mapping of their chromosomal locations on a phylogenetic tree reveals 27 different movements of genes to other chromosomes. Mapping of intron gains and losses onto the phylogenetic tree reveals that the last common ancestral gene of the family had five introns, which are inferred to have been lost 70 times independently during evolution of the family. In addition, seven intron gains are revealed, three of which are fairly recent. Comparisons with 20 family members in the C. briggsae genome confirms these patterns, including two intron losses in C. briggsae since the species split. There are 14 clear C. elegans orthologs for these 20 genes, whose average amino acid divergence of 68% allows estimation of 85 gene duplications in the C. elegans lineage since the species split. The absence of six orthologs in C. elegans also indicates that gene loss occurs; consideration of all deletions and terminal truncations of srh pseudogenes reveals that large deletions are common. Together these observations provide insight into the evolutionary dynamics of this compact animal genome.

Amino Acid Sequence↗