Decapterus maruadsi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA898455 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR22558419.fastq.gz | Fastqsanger.gz |
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Project description:Decapterus macrosoma Transcriptome or Gene expression
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Project description:Decapterus maruadsi isolate:Dmar-042203 Genome sequencing
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Project description:Sexual growth dimorphism is a common phenomenon in teleost fish and has led to many reproductive strategies. Growth- and sex-related gene research in teleost fish would broaden our understanding of the process. In this study, transcriptome sequencing of shortfin scad Decapterus macrosoma was performed for the first time, and a high-quality reference transcriptome was constructed. After identification and assembly, a total of 58,475 nonredundant unigenes were obtained with an N50 length of 2,266 bp, and 28,174 unigenes were successfully annotated with multiple public databases. BUSCO analysis determined a level of 92.9% completeness for the assembled transcriptome. Gene expression analysis revealed 2,345 differentially expressed genes (DEGs) in the female and male D. macrosoma, 1,150 of which were female-biased DEGs, and 1,195 unigenes were male-biased DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the DEGs were mainly involved in biological processes including protein synthesis, growth, rhythmic processes, immune defense, and vitellogenesis. Then, we identified many growth- and sex-related genes, including Igf, Fabps, EF-hand family genes, Zp3, Zp4 and Vg. In addition, a total of 19,573 simple sequence repeats (SSRs) were screened and identified from the transcriptome sequences. The results of this study can provide valuable information on growth- and sex-related genes and facilitate further exploration of the molecular mechanism of sexual growth dimorphism.
| S-EPMC9651050 | biostudies-literature
Project description:There are relatively few studies on parasite fauna of marine fishes in Philippine waters. This study aimed to determine the prevalence of marine ascaridoid infection in Decapterus species in Balayan Bay and Tayabas Bay. A total of 371 fishes belonging to three different species of Decapterus (D. tabl [n = 130], D. macrosoma [n = 121], and D. maruadsi [n = 120]) were collected. Ascaridoid parasite larvae were found in all fish host species, with an overall fish infection rate of 22%. The highest infection rate was observed in D. tabl (27.69%), followed by D. macrosoma (19%), and then D. maruadsi (17.50%). Moreover, a higher prevalence of infection was detected in Tayabas Bay (27.57%) than in Balayan Bay (15.59%). Molecular analyses based on the ITS2 and 18S rRNA gene supported the identification of the larvae into two species: Anisakis typica and Raphidascaris (Ichthyascaris) lophii. This is the first report of the genetic identification of these two helminth parasites in Decapterus fish species in the Philippines. Paucity in the database of Philippine marine fish parasites warrants more research efforts, especially concerning economically important fish species with implications to food safety and food security.
| S-EPMC9400525 | biostudies-literature
Project description:Decapterus maruadsi is one of the representative offshore fish in the Western Pacific. Since the last century, it has become a commercially valuable marine fishery species in the Western Pacific region. Despite its high economic value, there is still a lack of high-quality reference genome of D. maruadsi in germplasm resource evaluation research. Here we report a chromosome-level reference genome of D. maruadsi based on Nanopore sequencing and Hi-C technologies. The whole genome was assembled through 169 contigs with a total length of 723.69 Mb and a contig N50 length of 24.67 Mb. By chromosome scaffolding, 23 chromosomes with a total length of 713.58 Mb were constructed. In addition, a total of 199.49 Mb repetitive elements, 33,515 protein-coding genes, and 6,431 ncRNAs were annotated in the reference genome. This reference genome of D. maruadsi will provide a solid theoretical basis not only for the subsequent development of genomic resources of D. maruadsi but also for the formulation of policies related to the protection of D. maruadsi.
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Project description:The objective of the present study was to investigate the xanthine oxidase (XO) inhibitory effects of peptides purified and identified from round scad (Decapterus maruadsi) hydrolysates (RSHs). In this study, RSHs were obtained by using three proteases (neutrase, protamex and alcalase). Among them, the RSHs of 6-h hydrolysis by neutrase displayed the strongest XO inhibitory activity and had an abundance of small peptides (<500 Da). Four novel peptides were purified by immobilized metal affinity chromatography and identified by nano-high-performance liquid chromatography mass/mass spectrometry. Their amino acid sequences were KGFP (447.53 Da), FPSV (448.51 Da), FPFP (506.59 Da) and WPDGR (629.66 Da), respectively. Then the peptides were synthesized to evaluate their XO inhibitory activity. The results indicated that the peptides of both FPSV (5 mM) and FPFP (5 mM) exhibited higher XO inhibitory activity (22.61 ± 1.81% and 20.09 ± 2.41% respectively). Fluorescence spectra assay demonstrated that the fluorescence quenching mechanism of XO by these inhibitors (FPSV and FPFP) was a static quenching procedure. The study of inhibition kinetics suggested that the inhibition of both FPSV and FPFP was reversible, and the type of their inhibition was a mixed one. Molecular docking revealed the importance of π-π stacking between Phe residue (contained in peptides) and Phe914 (contained in the XO) in the XO inhibitory activity of the peptides.
| S-EPMC8538066 | biostudies-literature
Project description:A genomic overview of in vivo binding of a transcription factor Tbx6b in the ascidian early gastrula embryo.
2010-03-09 | GSE17694 | GEO
Project description:A genomic overview of in vivo binding of a transcription factor SoxC in the ascidian early gastrula embryo.
2010-03-09 | GSE17692 | GEO