Draft genome sequence data of Urechis unicinctus, a marine echiuroid worm.
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ABSTRACT:
SUBMITTER: Jiao X
PROVIDER: S-EPMC8081933 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundSulfide is a common toxin to animals and is abundant in coastal and aquatic sediments. Sulfur dioxygenase (SDO) is thought to be the key enzyme involved in sulfide oxidation in some organisms. The echiuran worm, Urechis unicinctus, inhabits coastal sediment and tolerates high concentrations of sulfide. The SDO is presumably important for sulfide tolerance in U. unicinctus.ResultsThe full-length cDNA of SDO from the echiuran worm U. unicinctus, proven to be located in the mitochondria, was cloned and the analysis of its sequence suggests that it belongs to the metallo-β-lactamase superfamily. The enzyme was produced using an E. coli expression system and the measured activity is approximately 0.80 U mg protein(-1). Furthermore, the expression of four sub-segments of the U. unicinctus SDO was accomplished leading to preliminary identification of functional domains of the enzyme. The identification of the conserved metal I (H113, H115, H169 and D188), metal II (D117, H118, H169 and H229) as well as the potential glutathione (GSH) (R197, Y231, M279 and I283) binding sites was determined by enzyme activity and GSH affinity measurements. The key residues responsible for SDO activity were identified by analysis of simultaneous mutations of residues D117 and H118 located close to the metal II binding site.ConclusionThe recombinant SDO from U. unicinctus was produced, purified and characterized. The metal binding sites in the SDO were identified and Y231 recognized as the mostly important amino acid residue for GSH binding. Our results show that SDO is located in the mitochondria where it plays an important role in sulfide detoxification of U. unicinctus.
| S-EPMC3846777 | biostudies-literature
Project description:BackgroundEchiurida is one of the most intriguing major subgroups of annelida because, unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of echiurid species can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development.ResultsA total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66% of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40%). The completeness of the transcriptome assembly was assessed using benchmarking universal single-copy orthologs; 75.7% of the single-copy orthologs were presented in our transcriptome database. We observed 3 distinct patterns of global transcriptome profiles from 14 developmental stages and identified 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells.ConclusionsWe present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.
| S-EPMC5863216 | biostudies-literature
Project description:BackgroundReal-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes.ResultsIn this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data.ConclusionOur study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.
| S-EPMC10170059 | biostudies-literature
Project description:Urechis unicinctus strain:echiuran worm Transcriptome or Gene expression
| PRJNA232444 | ENA
Project description:Urechis unicinctus, an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furthermore, the worm can tolerate and utilize well-known toxicant-sulfide. However, knowledge is limited on the molecular mechanism of U. unicinctus responding to sulfide due to deficiency of its genetic information.In this study, we performed Illumina sequencing to obtain the first Urechis unicinctus transcriptome data. Sequenced reads were assembled and then annotated using blast searches against Nr, Nt, Swiss-Prot, KEGG and COG. The clean tags from four digital gene expression (DGE) libraries were mapped to the U. unicinctus transcriptome. DGE analysis and functional annotation were then performed to reveal its response to sulfide. The expressions of 12 candidate genes were validated using quantitative real-time PCR. The results of qRT-PCR were regressed against the DGE analysis, with a correlation coefficient and p-value reported for each of them.Here we first present a draft of U. unicinctus transcriptome using the Illumina HiSeq(TM) 2000 platform and 52,093 unique sequences were assembled with the average length of 738 bp and N50 of 1131 bp. About 51.6 % of the transcriptome were functionally annotated based on the databases of Nr, Nt, Swiss-Prot, KEGG and COG. Then based on the transcriptome, the digital gene expression analysis was conducted to examine the transcriptional response to sulfide during 6, 24 and 48 h exposure, and finally 1705, 1181 and 1494 tag-mapped genes were identified as differentially expressed genes in the 6-h, 24-h and 48-h libraries, then were further subjected to pathway analyses.In the DGE database of U. unicinctus, the alterations in certain known sulfide-related pathways indicate similar changes in response to sulfide. For more than 80 % of the identified pathway members, this is the first report on their association with sulfide stress, among which glycolysis pathway and PIDD involving pathways were unique and discussed in details, and were thought to play important roles in the sulfide tolerance of U. unicinctus. All the results are helpful to explain the mechanism of sulfide tolerance and detoxification.
| S-EPMC4618349 | biostudies-literature
Project description:The larval segment formation and secondary loss in echiurans is a special phenomenon, which is considered to be one of the important characteristics in the evolutionary relationship between the Echiura and Annelida. To better understand the molecular mechanism of this phenomenon, we revealed the larval transcriptome profile of the echiuran worm Urechis unicinctus using RNA-Seq technology. Twelve cDNA libraries of U. unicinctus larvae, late-trochophore (LT), early-segmentation larva (ES), segmentation larva (SL), and worm-shaped larva (WL) were constructed. Totally 243,381 unigenes were assembled with an average length of 1125 bp and N50 of 1836 bp, and 149,488 unigenes (61.42%) were annotated. We obtained 70,517 differentially expressed genes (DEGs) by pairwise comparison of the larval transcriptome data at different developmental stages and clustered them into 20 gene expression profiles using STEM software. Based on the typical profiles during the larval segment formation and secondary loss, eight signaling pathways were enriched, and five of which, mTOR, PI3K-AKT, TGF-β, MAPK, and Dorso-ventral axis formation signaling pathway, were proposed for the first time to be involved in the segment formation. Furthermore, we identified 119 unigenes related to the segment formation of annelids, arthropods, and chordates, in which 101 genes were identified in Drosophila and annelids. The function of most segment polarity gene homologs (hedgehog, wingless, engrailed, etc.) was conserved in echiurans, annelids, and arthropods based on their expression profiles, while the gap and pair-rule gene homologs were not. Finally, we verified that strong positive signals of Hedgehog were indeed located on the boundary of larval segments using immunofluorescence. Data in this study provide molecular evidence for the understanding of larval segment development in echiurans and may serve as a blueprint for segmented ancestors in future research.
| S-EPMC6514800 | biostudies-literature
Project description:Echiura is a distinctive family of unsegmented sausage-shaped marine worms whose phylogenetic relationship still needs strong evidence from the phylogenomic analysis. In this family, Urechis unicinctus is known for its high nutritional and medicinal value and adaptation to harsh intertidal conditions. Herein, we combined PacBio long-read, short-read Illumina and Hi-C sequencing, generating a high-quality chromosome-level genome assembly of U. unicinctus. The assembled genome spans ~1,138.6 Mb with a scaffold N50 of 68.3 Mb, of which 1,113.8 Mb (97.82%) were anchored into 17 pseudo-chromosomes. The BUSCO analysis demonstrated the completeness of the genome assembly and gene model prediction are 93.5% and 91.5%, respectively. A total of 482.1 Mb repetitive sequences, 21,524 protein-coding genes, 1,535 miRNAs, 3,431 tRNAs, 124 rRNAs, and 348 snRNAs were annotated. This study significantly improves the quality of U. unicinctus genome assembly, sets the footsteps for molecular breeding and further study in genome evolution, genetic and molecular biology of U. unicinctus.
| S-EPMC10796407 | biostudies-literature
Project description:The human ?-site amyloid cleaving enzyme (BACE1) has been considered as an effective drug target for treatment of Alzheimer's disease (AD). In this study, Urechis unicinctus (U. unicinctus), which is a Far East specialty food known as innkeeper worm, ethanol extract was studied by bioassay-directed fractionation and isolation to examine its potential ?-site amyloid cleaving enzyme inhibitory and antimicrobial activity. The following compounds were characterized: hecogenin, cholest-4-en-3-one, cholesta-4,6-dien-3-ol, and hurgadacin. These compounds were identified by their mass spectrometry, ¹H, and 13C NMR spectral data, comparing those data with NIST/EPA/NIH Mass spectral database (NIST11) and published values. Hecogenin and cholest-4-en-3-one showed significant inhibitory activity against BACE1 with EC50 values of 116.3 and 390.6 µM, respectively. Cholesta-4,6-dien-3-ol and hurgadacin showed broad spectrum antimicrobial activity, particularly strongly against Escherichia coli (E. coli), Salmonella enterica (S. enterica), Pasteurella multocida (P. multocida), and Physalospora piricola (P. piricola), with minimal inhibitory concentration (MIC) ranging from 0.46 to 0.94 mg/mL. This is the first report regarding those four known compounds that were isolated from U. unicinctus and their anti-BACE1 and antimicrobial activity, highlighting the fact that known natural compounds may be a critical source of new medicine leads. These findings provide scientific evidence for potential application of those bioactive compounds for the development of AD drugs and antimicrobial agents.
| S-EPMC5867638 | biostudies-literature
Project description:Echiura is one of the most intriguing major subgroups of phylum Annelida because, unlike most other annelids, echiuran adults lack metameric body segmentation. Urechis unicinctus lives in U-shape burrows of soft sediments. Little is known about the molecular mechanisms underlying the development of U. unicinctus. Herein, we overviewed the developmental process from zygote to juvenile U. unicinctus using immunohistochemistry and F-actin staining for the nervous and muscular systems, respectively. Through F-actin staining, we found that muscle fibers began to form in the trochophore phase and that muscles for feeding were produced first. Subsequently, in the segmentation larval stage, the transversal muscle was formed in the shape of a ring in an anterior-to-posterior direction with segment formation, as well as a ventromedian muscle for the formation of a ventral nerve cord. After that, many muscle fibers were produced along the entire body and formed the worm-shaped larva. Finally, we investigated the spatiotemporal expression of Uun_st-mhc, Uun_troponin I, Uun_calponin, and Uun_twist genes found in U. unicinctus. During embryonic development, the striated and smooth muscle genes were co-expressed in the same region. However, the adult body wall muscles showed differential gene expression of each muscle layer. The results of this study will provide the basis for the understanding of muscle differentiation in Echiura.
| S-EPMC7178014 | biostudies-literature
Project description:BackgroundIn marine invertebrate life cycles, which often consist of planktonic larval and benthonic adult stages, settlement of the free-swimming larva to the sea floor in response to environmental cues is a key life cycle transition. Settlement is regulated by a specialized sensory-neurosecretory system, the larval apical organ. The neuroendocrine mechanisms through which the apical organ transduces environmental cues into behavioral responses during settlement are not fully understood yet.ResultsIn this study, a total of 54 neuropeptide precursors (pNPs) were identified in the Urechis unicinctus larva and adult transcriptome databases using local BLAST and NpSearch prediction, of which 10 pNPs belonging to the ancient eumetazoa, 24 pNPs belonging to the ancient bilaterian, 3 pNPs belonging to the ancient protostome, 9 pNPs exclusive in lophotrochozoa, 3 pNPs exclusive in annelid, and 5 pNPs only found in U. unicinctus. Furthermore, four pNPs (MIP, FRWamide, FxFamide and FILamide) which may be associated with the settlement and metamorphosis of U. unicinctus larvae were analysed by qRT-PCR. Whole-mount in situ hybridization results showed that all the four pNPs were expressed in the region of the apical organ of the larva, and the positive signals were also detected in the ciliary band and abdomen chaetae. We speculated that these pNPs may regulate the movement of larval cilia and chaeta by sensing external attachment signals.ConclusionsThis study represents the first comprehensive identification of neuropeptides in Echiura, and would contribute to a complete understanding on the roles of various neuropeptides in larval settlement of most marine benthonic invertebrates.
| S-EPMC7737342 | biostudies-literature