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The Pan African Medical Journal 2021
Topics: Animals; Humans; Intestines; Platyhelminths
PubMed: 34603590
DOI: 10.11604/pamj.2021.39.209.30820 -
Nucleic Acids Research Jan 2016WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project...
WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.
Topics: Animals; Caenorhabditis elegans; Databases, Genetic; Genes, Helminth; Genome, Helminth; Genomics; Molecular Sequence Annotation; Nematoda; Platyhelminths; Software
PubMed: 26578572
DOI: 10.1093/nar/gkv1217 -
BMC Veterinary Research May 2021Platyhelminth infections of livestock can result in considerable economic losses. This study aims to evaluate the spatial frequency of cystic echinococcosis (CE),...
BACKGROUND
Platyhelminth infections of livestock can result in considerable economic losses. This study aims to evaluate the spatial frequency of cystic echinococcosis (CE), dicrocoeliasis, and fascioliasis in livestock slaughtered in Iran during the years 2015-2019 and estimate direct costs associated with organ condemnation due to these parasites.
METHODS
Abattoir data from 413 abattoirs representing all 31 Iranian provinces were collected from the Iran Veterinary Organization. Infection prevalence was calculated per year at the province level. The Local Moran's I statistic was performed to evaluate spatial autocorrelation of animals positive at slaughter for the years 2015-2019. Direct costs associated with condemned livers were calculated for each parasitic condition, with costs associated with condemned lungs also included for CE.
RESULTS
Overall prevalence values for the study timeframe were as follows: sheep and goat fascioliasis 1.56% (95% CI: 1.56-1.56%), cattle fascioliasis 3.86% (95% CI: 3.85-3.88%), sheep and goat dicrocoeliasis 4.63% (95% CI: 4.62-4.63%), cattle dicrocoeliasis 3.08% (95% CI: 3.07-3.09%), sheep and goat CE 5.32% (95% CI: 5.32-5.33%), and cattle CE 7.26% (95% CI: 7.24-7.28%). Northwest Iran had the highest prevalence of CE and fascioliasis. High infection areas for Dicrocoelium spp. included the provinces of Zanjan, Gilan, Qazvin, and Tehran, which are located in northern Iran. Direct economic losses for sheep and goat fascioliasis, dicrocoeliasis, and CE for the study period were US$13,842,759, US$41,771,377, and US$22,801,054, respectively. Direct economic losses for cattle fascioliasis, dicrocoeliasis, and CE for the study period were US$1,989,200, US$1,668,986, and US$2,656,568, respectively.
CONCLUSION
Our findings provide valuable data for future monitoring of these important parasitic diseases in Iranian livestock. Disease control strategies are required to reduce the economic and public health impact of these platyhelminths.
Topics: Abattoirs; Animals; Cattle; Cattle Diseases; Dicrocoeliasis; Dicrocoelium; Echinococcosis; Echinococcus; Fasciola; Fascioliasis; Goat Diseases; Goats; Iran; Livestock; Sheep; Sheep Diseases; Zoonoses
PubMed: 33952280
DOI: 10.1186/s12917-021-02888-9 -
Nature Communications Jun 2022Many species with separate male and female individuals (termed 'gonochorism' in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when...
Many species with separate male and female individuals (termed 'gonochorism' in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes recently evolved gonochorism from ancestral hermaphroditism), and roundworms (Nematoda) which have undergone independent translocations of different autosomes. Although neither the evolution of gonochorism nor translocations fusing ancestrally autosomal regions to sex chromosomes causes inevitable loss of recombination, we document that formerly recombining regions show genomic signatures of recombination suppression in both taxa, and become strongly genetically degenerated, with a loss of most genes. Comparisons with hermaphroditic flatworm transcriptomes show masculinisation and some defeminisation in schistosome gonad gene expression. We also find evidence that evolution of sex-linkage in nematodes is accompanied by transcriptional changes and dosage compensation. Our analyses also identify sex-linked genes that could assist future research aimed at controlling some of these important parasites.
Topics: Animals; Dosage Compensation, Genetic; Evolution, Molecular; Female; Male; Nematoda; Platyhelminths; Sex Chromosomes; Transcriptome
PubMed: 35688815
DOI: 10.1038/s41467-022-30578-z -
GigaScience Apr 2019Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular...
BACKGROUND
Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.
FINDINGS
To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17-kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.
CONCLUSIONS
Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
Topics: Animals; Computational Biology; Gene Expression Profiling; Genome Size; Genome, Helminth; Genome, Mitochondrial; Genomics; Molecular Sequence Annotation; Phenotype; Platyhelminths; Repetitive Sequences, Nucleic Acid; Transcriptome; Web Browser
PubMed: 30953569
DOI: 10.1093/gigascience/giz023 -
BMC Research Notes Jun 2014Clonorchiasis, which is primarily caused by liver fluke (Platyhelminthes), is a fatal infectious disease that is mainly associated with bile duct malignancy and the...
BACKGROUND
Clonorchiasis, which is primarily caused by liver fluke (Platyhelminthes), is a fatal infectious disease that is mainly associated with bile duct malignancy and the subsequent development of cholangiocarcinoma. Thus, a genomic approach now represents an important step to further our knowledge of biology and the pathology of these parasites. The results of expressed sequence tags (ESTs) sequencing need to be well organized into databases to provide an integrated set of tools and functional information.
FINDINGS
Here, the ClonorESTdb database represents a collection of Clonorchis sinensis ESTs that is intended as a resource for parasite functional genomics. A total of 55,736 successful EST sequences, which are cleaned and clustered into non-redundant 13,305 C. sinensis assembled EST sequences (6,497 clusters and 6,808 singletons), were obtained from three in-house prepared cDNA libraries of C. sinensis at different developmental stages. The assembled consensus sequences were annotated using the BLAST algorithm or/and hmm against NCBI NR, UniProt, KEGG and InterProScan. The ClonorESTdb database provides functional annotation, their expression profiles, tandem repeats and putative single nucleotide polymorphisms with utility tools such as local BLAST search and text retrieval.
CONCLUSIONS
This resource enables the researcher to identify and compare expression signatures under different biological stages and promotes ongoing parasite drug and vaccine development and biological research.Database URL:http://pathod.cdc.go.kr/clonorestdb/.
Topics: Animals; Clonorchis sinensis; Computational Biology; Databases, Genetic; Expressed Sequence Tags; Gene Expression Profiling; Gene Library; Genomics; Information Storage and Retrieval; Internet; Life Cycle Stages; Polymorphism, Single Nucleotide
PubMed: 24957044
DOI: 10.1186/1756-0500-7-388 -
ELife Apr 2015Understanding the evolutionary relationships between species could help researchers select better model organisms to study in the laboratory.
Understanding the evolutionary relationships between species could help researchers select better model organisms to study in the laboratory.
Topics: Animals; Biological Evolution; Cell Nucleus; Genome; Platyhelminths
PubMed: 25879271
DOI: 10.7554/eLife.07431 -
BMC Genomics Jul 2020Cestoda is a class of endoparasitic worms in the flatworm phylum (Platyhelminthes). During the course of their evolution cestodes have evolved some interesting aspects,...
BACKGROUND
Cestoda is a class of endoparasitic worms in the flatworm phylum (Platyhelminthes). During the course of their evolution cestodes have evolved some interesting aspects, such as their increased reproductive capacity. In this sense, they have serial repetition of their reproductive organs in the adult stage, which is often associated with external segmentation in a developmental process called strobilation. However, the molecular basis of strobilation is poorly understood. To assess this issue, an evolutionary comparative study among strobilated and non-strobilated flatworm species was conducted to identify genes and proteins related to the strobilation process.
RESULTS
We compared the genomic content of 10 parasitic platyhelminth species; five from cestode species, representing strobilated parasitic platyhelminths, and five from trematode species, representing non-strobilated parasitic platyhelminths. This dataset was used to identify 1813 genes with orthologues that are present in all cestode (strobilated) species, but absent from at least one trematode (non-strobilated) species. Development-related genes, along with genes of unknown function (UF), were then selected based on their transcriptional profiles, resulting in a total of 34 genes that were differentially expressed between the larval (pre-strobilation) and adult (strobilated) stages in at least one cestode species. These 34 genes were then assumed to be strobilation related; they included 12 encoding proteins of known function, with 6 related to the Wnt, TGF-β/BMP, or G-protein coupled receptor signaling pathways; and 22 encoding UF proteins. In order to assign function to at least some of the UF genes/proteins, a global gene co-expression analysis was performed for the cestode species Echinococcus multilocularis. This resulted in eight UF genes/proteins being predicted as related to developmental, reproductive, vesicle transport, or signaling processes.
CONCLUSIONS
Overall, the described in silico data provided evidence of the involvement of 34 genes/proteins and at least 3 developmental pathways in the cestode strobilation process. These results highlight on the molecular mechanisms and evolution of the cestode strobilation process, and point to several interesting proteins as potential developmental markers and/or targets for the development of novel antihelminthic drugs.
Topics: Animals; Cestoda; Evolution, Molecular; Gene Expression Profiling; Genes, Helminth; Helminth Proteins; Phylogeny
PubMed: 32677885
DOI: 10.1186/s12864-020-06878-3 -
Philosophical Transactions of the Royal... Oct 2019Flatworms can very rapidly attach to and detach from many substrates. In the presented work, we analysed the adhesive system of the marine proseriate flatworm Minona...
Flatworms can very rapidly attach to and detach from many substrates. In the presented work, we analysed the adhesive system of the marine proseriate flatworm Minona ileanae. We used light-, scanning- and transmission electron microscopy to analyse the morphology of the adhesive organs, which are located at the ventral side of the tail-plate. We performed transcriptome sequencing and differential RNA-seq for the identification of tail-specific transcripts. Using in situ hybridization expression screening, we identified nine transcripts that were expressed in the cells of the adhesive organs. Knock-down of five of these transcripts by RNA interference led to a reduction of the animal's attachment capacity. Adhesive proteins in footprints were confirmed using mass spectrometry and antibody staining. Additionally, lectin labelling of footprints revealed the presence of several sugar moieties. Furthermore, we determined a genome size of about 560 Mb for M. ileanae. We demonstrated the potential of Oxford Nanopore sequencing of genomic DNA as a cost-effective tool for identifying the number of repeats within an adhesive protein and for combining transcripts that were fragments of larger genes. A better understanding of the molecules involved in flatworm bioadhesion can pave the way towards developing innovative glues with reversible adhesive properties. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.
Topics: Animals; Cell Adhesion; Helminth Proteins; Platyhelminths; RNA Interference; Transcription, Genetic
PubMed: 31495318
DOI: 10.1098/rstb.2019.0194 -
Comptes Rendus Biologies Feb 2012The aim of this study was to characterize for the first time spermatogenesis and spermiogenesis in the freshwater planarian Schmidtea mediterranea using both light and...
The aim of this study was to characterize for the first time spermatogenesis and spermiogenesis in the freshwater planarian Schmidtea mediterranea using both light and electron microscopy. Starting from the border towards the testis lumen we found types I and II spermatogonia, clusters of primary and secondary spermatocytes, spermatids and free spermatozoa. Light microscope observations show that type I spermatogonia have a large and pale nucleus whereas type II spermatogonia are significantly smaller than the one of type I, and show a darker and central bulky nucleus. At the ultrastructure level, both type I and type II spermatogonia are characterized by a wide nucleus with scanty cytoplasm containing free ribosomes, mitochondria and a dense chromatoid body whereas endoplasmic reticulum and Golgi complex were not observed. The cytoplasm of primary and secondary spermatocytes displays numerous free ribosomes and many endoplasmic reticulum cisternae and Golgi complexes, suggesting that the development of these organelles during spermatogenesis might contribute to the synthesis of hormones and proteins such as testosterone, transcription factors and tubulin. Mature spermatozoa structure closely resembles those of other freshwater triclads with a nucleus, a single fused mitochondrion, a row of cortical microtubules and a pair of flagella conforming to the 9+'1' microtubule pattern described for other Platyhelminthes.
Topics: Animals; Male; Microscopy, Electron; Platyhelminths; Spermatogenesis; Spermatozoa
PubMed: 22325561
DOI: 10.1016/j.crvi.2011.11.005