159 research outputs found
Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes
No full textComparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi
Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites
No full textParasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
No full textABSTRACT: BACKGROUND: Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic in its new host than in its native one, and is thought to threaten the endangered An. anguilla across its range. The molecular bases for the increased pathogenicity of the nematodes in their new hosts is not known. RESULTS: A reference transcriptome was assembled for A. crassus from Roche 454 pyrosequencing data. Raw reads (756,363 total) from nematodes from An. japonica and An. anguilla hosts were filtered for likely host contaminats and ribosomal RNAs. The remaining 353,055 reads were assembled into 11,372 contigs of a high confidence assembly (spanning 6.6 Mb) and an additional 21,153 singletons and contigs of a lower confidence assembly (spanning an additional 6.2 Mb). Roughly 55% of the high condence assembly contigs were annotated with domain- or protein sequence similarity derived functional information. Sequences conserved only in nematodes, or unique to A. crassus were more likely to have secretory signal peptides. Thousands of high quality single nucleotide polymorphisms were identified, and coding polymorphism was correlated with diffrential expression between individual nematodes. Transcripts identfied as being under positive selection were enriched in peptidases. Enzymes involved in energy metabolism were enriched in the set of genes differentially expressed between European and Asian A. crassus. CONCLUSIONS: The reference transcriptome of A. crassus is of high quality, and will serve as a basis for future work on the invasion biology of this important parasite. The polymorphisms identied will provide a key tool set for analysis of population structure and identication of genes likely to be involved in increased pathogenicity in European eel hosts. The identication of peptidases under positive selection is a first step in this programme
prot4EST: translating expressed sequence tags from neglected genomes
No full textThe genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects
The genome of Romanomermis culicivorax:revealing fundamental changes in the core developmental genetic toolkit in Nematoda
No full textThe genetics of development in the nematode Caenorhabditis elegans has been described in exquisitedetail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and theEnoplea. While the development of many chromadorean species resembles closely that of C. elegans,enoplean nematodes show markedly different patterns of early cell division and cell fate assignment.Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the geneticcircuitry underpinning development in this species has not been explored
Operon conservation and the evolution of trans-splicing in the phylum Nematoda
No full textThe nematode Caenorhabditis elegans is unique among model animals in that many of its genes are cotranscribed as polycistronic pre-mRNAs from operons. The mechanism by which these operonic transcripts are resolved into mature mRNAs includes trans-splicing to a family of SL2-like spliced leader exons. SL2-like spliced leaders are distinct from SL1, the major spliced leader in C. elegans and other nematode species. We surveyed five additional nematode species, representing three of the five major clades of the phylum Nematoda, for the presence of operons and the use of trans-spliced leaders in resolution of polycistronic pre-mRNAs. Conserved operons were found in Pristionchus pacificus, Nippostrongylus brasiliensis, Strongyloides ratti, Brugia malayi, and Ascaris suum. In nematodes closely related to the rhabditine C. elegans, a related family of SL2-like spliced leaders is used for operonic transcript resolution. However, in the tylenchine S. ratti operonic transcripts are resolved using a family of spliced leaders related to SL1. Non-operonic genes in S. ratti may also receive these SL1 variants. In the spirurine nematodes B. malayi and A. suum operonic transcripts are resolved using SL1. Mapping these phenotypes onto the robust molecular phylogeny for the Nematoda suggests that operons evolved before SL2-like spliced leaders, which are an evolutionary invention of the rhabditine lineage
Next-generation nematode genomes
No full textINTRODUCTION:
The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and
understanding the genome of this model organism has led to many insights about all
animals. Although eleven nematode genomes have been published so far and approximately
twenty more are under way, the vast majority of the genomes of this incredibly diverse
phylum remain unexplored. Next-generation sequencing has made it possible to generate
large amounts of genome sequence data in a few days at a fraction of the cost of traditional
Sanger-sequencing. However, assembling and annotating these data into genomic resources
remains a challenge because of the short reads, the quality issues in these kinds of data, and
the presence of contaminants and co-bionts in uncultured samples. In this thesis, I describe
the process of creating high quality draft genomes and annotation resources for four
nematode species representing three of the five major nematode clades: Caenorhabditis sp. 5,
Meloidogyne floridensis, Dirofilaria immitis, and Litomosoides sigmodontis. I describe the new
approaches I developed for visualising contamination and co-bionts, and I present the
details of the robust workflow I devised to deal with the problems of generating low-cost
genomic resources from Illumina short-read sequencing.
RESULTS:
The draft genome assemblies created using the workflow described in this thesis are
comparable to the draft nematode genomes created using Sanger sequencing. Armed with
these genomes, I was able to answer two evolutionary genomics questions at very different
scales. The first question was whether any non-coding elements were deeply conserved at
the level of the whole phylum. Such elements had previously been hypothesised to be
responsible for the phylum body plan in vertebrates, insects, and nematodes. I used twenty
nematode genomes in several whole-genome alignments and concluded that no such
elements were conserved across the whole phylum. The second question addressed the
origins of the highly destructive plant-parasitic root-knot nematode Meloidogyne incognita.
Comparisons with the newly sequenced Meloidogyne floridensis genome revealed the
complex hybrid origins of both species, undermining previous assumptions about the rarity
of hybrid speciation in animals.
CONCLUSIONS:
This thesis demonstrates the role of next-generation sequencing in democratising genome
sequencing projects. Using the sequencing strategies, workflows, and tools described here,
one can rapidly create genomic resources at a very low cost, even for unculturable
metazoans. These genomes can be used to understand the evolutionary history of a genus or
a phylum, as shown
GC vs coverage plot of A. nasoniae genome assembly, created using Blobtools.
No full textGC vs coverage plot of A. nasoniae genome assembly, created using Blobtools (Laetsch and Blaxter, 2017)X axis: GC content of componentY axis: Read depth of componentBlob colour: Green = main chromosome; Orange = circular plasmid; Purple = linear plasmidSize of blob indicates relative size of element in bp.Laetsch DR and Blaxter ML. BlobTools: Interrogation of genome assemblies [version 1; peer review: 2 approved with reservations]. F1000Research 2017, 6:1287 (https://doi.org/10.12688/f1000research.12232.1)</div
Immunological genomics of Brugia malayi:filarial genes implicated in immune evasion and protective immunity
No full textFilarial nematodes are metazoan parasites with genome sizes of> 100 million base pairs, probably encoding 15 000-20 000 genes. Within this considerable gene complement, it seems likely that filariae have evolved a spectrum of immune evasion products which underpin their ability to live for many years within the human host. Moreover, no suitable vaccine currently exists for human filarial diseases, and few markers have yet been established for diagnostic use. In this review, we bring together biochemical and immunological data on prominent filarial proteins with the exciting new information provided by the Filarial Genome Project's expressed sequence tag (EST) database. In this discussion, we focus on those genes with the highest immunological profile, such as inhibitors of host enzymes, cytokine homologues and stage-specific surface proteins, as well as products associated with the mosquito-borne infective larva which offer the best opportunity for an anti-filarial vaccine. These gene products provide a fascinating glimpse of the molecular repertoire which helminth parasites have evolved to manipulate and evade the mammalian immune response
The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets
No full textThe heartworm Dirofilaria immitis is an important parasite of dogs. Transmitted by mosquitoes in warmer climatic zones, it is spreading across southern Europe and the Americas at an alarming pace. There is no vaccine, and chemotherapy is prone to complications. To learn more about this parasite, we have sequenced the genomes of D. immitis and its endosymbiont Wolbachia. We predict 10,179 protein coding genes in the 84.2 Mb of the nuclear genome, and 823 genes in the 0.9-Mb Wolbachia genome. The D. immitis genome harbors neither DNA transposons nor active retrotransposons, and there is very little genetic variation between two sequenced isolates from Europe and the United States. The differential presence of anabolic pathways such as heme and nucleotide biosynthesis hints at the intricate metabolic interrelationship between the heartworm and Wolbachia. Comparing the proteome of D. immitis with other nematodes and with mammalian hosts, we identify families of potential drug targets, immune modulators, and vaccine candidates. This genome sequence will support the development of new tools against dirofilariasis and aid efforts to combat related human pathogens, the causative agents of lymphatic filariasis and river blindness
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