Draft Genome Sequence of Streptomyces sp. Strain PAM3C, a Prospective Probiotic Agent Isolated from the Gut of the Bay Scallop, Argopecten purpuratus (Lamarck, 1819).
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ABSTRACT:
SUBMITTER: Serrano W
PROVIDER: S-EPMC8459655 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops.FindingsA total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly.ConclusionsWe generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.
| S-EPMC5905365 | biostudies-literature
Project description:Two Vibrio strains (VPAP36 and VPAP40) were isolated from moribund-settled larvae of the Chilean scallop Argopecten purpuratus during vibriosis outbreaks that occurred in two commercial scallop larvae hatcheries located in the Inglesa and Tongoy bays in Northern Chile. The strains were identified as Vibrio chagasii using phenotypic characterization and whole genome sequence analysis. Both strains exhibited the phenotypic properties associated with virulence, gelatin hydrolysis and β-hemolysis, whereas only VPAP36 produced phospholipase and only VPAP40 produced caseinase. The whole genome analysis showed that the strains harbored genes encoding for the virulence factors, the EPS type II secretion system, and Quorum Sensing (auto-inductor 1 and auto-inductor 2), whereas genes encoding a metalloproteinase and a capsular polysaccharide were detected only in the VPAP40 genome. When challenge bioassays using healthy 11-day-old scallop larvae were performed, the V. chagasii VPAP36 and VPAP40 strains exhibited significant (p < 0.05) differences in their larval lethal activity, producing, after 48 h, larval mortalities of 65.51 ± 4.40% and 28.56 ± 5.35%, respectively. Otherwise, the cell-free extracellular products of the VPAP36 and VPAP40 strains produced larval mortalities of 20.86 ± 2.40% and 18.37 ± 2.40%, respectively, after 48 h of exposure. This study reports for the first time the isolation of V. chagasii from the massive larval mortalities of the farmed scallop (Argopecten purpuratus) in Chile, and demonstrates the pathogenic activity of V. chagasii towards the Chilean scallop, the second most important species for Chilean mariculture.
| S-EPMC9964487 | biostudies-literature
Project description:Despite the importance of the Peruvian scallop Argopecten purpuratus as a major cultivated species, information on its microbiota is limited. Here, we provide a high-throughput sequencing data analysis of 16S rRNA gene amplicons from the distal intestine of A. purpuratus Geographical and seasonal variation of the indigenous gut microbiota is shown.
| S-EPMC7171220 | biostudies-literature
Project description:The two subspecies of Atlantic bay scallop (Argopecten irradians), A. i. irradians and A. i. concentricus, are economically important aquacultural species in northern and southern China. Here, we performed the whole-genome sequencing, assembly, and gene annotation and produced draft genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of raw reads were generated from Illumina Hiseq and PacBio platforms for A. i. irradians and A. i. concentricus, respectively. Draft genomes of 835.7?Mb and 874.82?Mb were assembled for the two subspecies, accounting for 83.9% and 89.79% of the estimated sizes of their corresponding genomes, respectively. The contig N50 and scaffold N50 were 78.54?kb and 1.53?Mb for the A. i. irradians genome, and those for the A. i. concentricus genome were 63.73?kb and 1.25?Mb. Moreover, 26,777 and 25,979 protein-coding genes were predicted for A. i. irradians and A. i. concentricus, respectively. These valuable genome assemblies lay a solid foundation for future theoretical studies and provide guidance for practical scallop breeding.
| S-EPMC7090048 | biostudies-literature
Project description:Carotenoids are commonly deposited in the gonads of marine bivalves but rarely in their adductor muscles. An orange-adductor variant was identified in our breeding program for the bay scallop Argopecten irradians. In the present study, bay scallop genome survey sequencing was conducted, followed by genotyping by sequencing (GBS)-based case-control association analysis in a selfing family that exhibited segregation in adductor color. K-mer analysis (K=17) revealed that the bay scallop genome is about 990 Mb in length. De novo assembly produced 217,310 scaffold sequences, which provided 72.1% coverage of the whole genome and covered 72,187 transcripts, thereby yielding the most informative sequence resource for bay scallop to date. The average carotenoid content of the orange-adductor progenies was significantly higher than that of the white-adductor progenies. Thus, 20 individuals of each subgroup were sampled for case-control analysis. As many as 15,224 heterozygous loci were identified in the parent, among which 9280 were genotyped in at least 10 individuals of each of the two sub-groups. Association analysis indicated that 126 SNPs were associated with carotenoid accumulation in the adductor muscle and that 88 of these were significantly enriched on 28 scaffolds (FDR controlled P < 0.05). The SNPs and genes located on these scaffolds can serve as valuable candidates for further research into the mechanisms by which marine bivalves accumulate carotenoids in their adductor muscles.
| S-EPMC5535694 | biostudies-literature
Project description:We have a growing understanding of the light-sensing organs and light-influenced behaviours of animals with distributed visual systems, but we have yet to learn how these animals convert visual input into behavioural output. It has been suggested they consolidate visual information early in their sensory-motor pathways, resulting in them being able to detect visual cues (spatial resolution) without being able to locate them (spatial vision). To explore how an animal with dozens of eyes processes visual information, we analysed the responses of the bay scallop Argopecten irradians to both static and rotating visual stimuli. We found A. irradians distinguish between static visual stimuli in different locations by directing their sensory tentacles towards them and were more likely to point their extended tentacles towards larger visual stimuli. We also found that scallops track rotating stimuli with individual tentacles and with rotating waves of tentacle extension. Our results show, to our knowledge for the first time that scallops have both spatial resolution and spatial vision, indicating their sensory-motor circuits include neural representations of their visual surroundings. Exploring a wide range of animals with distributed visual systems will help us learn the different ways non-cephalized animals convert sensory input into behavioural output.
| S-EPMC8580434 | biostudies-literature
Project description:Okadaic acid (OA) is produced by dinoflagellates during harmful algal blooms and is a diarrhetic shellfish poisoning toxin. This toxin is particularly problematic for bivalves that are cultured for human consumption. This study aimed to reveal the effects of exposure to OA on the immune responses of bay scallop, Argopecten irradians. Various immunological parameters were assessed (total hemocyte counts (THC), reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH), lactate dehydrogenase (LDH), and nitric oxide (NO) in the hemolymph of scallops at 3, 6, 12, 24, and 48 h post-exposure (hpe) to different concentrations of OA (50, 100, and 500 nM). Moreover, the expression of immune-system-related genes (CLT-6, FREP, HSP90, MT, and Cu/ZnSOD) was also measured. Results showed that ROS, MDA, and NO levels and LDH activity were enhanced after exposure to different concentrations of OA; however, both THC and GSH decreased between 24-48 hpe. The expression of immune-system-related genes was also assessed at different time points during the exposure period. Overall, our results suggest that exposure to OA had negative effects on immune system function, increased oxygenic stress, and disrupted metabolism of bay scallops.
| S-EPMC6272952 | biostudies-literature
Project description:The thiazolidinedione 49 (TD49) is an effective algaecide against harmful algae; however, its potential effects on the immune function of the edible bay scallop are unclear. Therefore, the present work studied the effects of TD49 on the immune response in bay scallop by evaluating activities of acid phosphatase (ACP), alkaline phosphatase (ALP), and superoxide dismutase (SOD), as well as nitric oxide (NO) levels, total protein content, and expression of immune genes (CTL-6, PGRP, PrxV, MT, and Cu/Zn-SOD) at 3-48 h post-exposure (hpe) to TD49. The activities of ACP and ALP significantly increased in TD49-treated groups at 3-24 hpe, whereas NO levels decreased significantly in 0.58 and 0.68 μM of TD49 at 6-24 hpe, after which the level was similar to that in the untreated control. Moreover, SOD activity significantly increased in all three concentration groups at 3-6 hpe, while it decreased at 12 hpe in the 0.68 μM TD49 treatment group. Notably, total protein content increased with TD49 treatment at each time interval. The results revealed that variable effects on the expression of immune-related genes were observed after treatment with TD49. The findings demonstrate that exposure of scallops to TD49 changes immune responses and expression of immune-related genes. We hypothesize that TD49 may disrupt immune system in bay scallop. The current investigation highlights the potential negative effects of using TD49 as an algaecide on marine economic bivalves to control harmful algal blooms in marine environments.
| S-EPMC6804249 | biostudies-literature
Project description:A new Vibrio strain, V7A, was isolated from the intestinal tract of the Peruvian scallop (Argopecten purpuratus). Strain V7A clusters within the Mediterranei clade of the genus Vibrio and has the potential to produce bacteriocin-like inhibitory substances (BLIS). Here, we report the draft genome sequence of Vibrio mediterranei strain V7A.
| S-EPMC5958249 | biostudies-literature
Project description:Domoic acid (DA), the main toxin responsible for Amnesic Shellfish Poisoning, frequently affects the marine resources of Chile and other countries across the South Pacific, thus becoming a risk for human health. One of the affected resources is the scallop Argopecten purpuratus. Even though this species has a high commercial importance in Northern Chile and Peru, the characteristics of its DA depuration are not known. In this work, the DA depuration was studied by means of two experiments: one in controlled (laboratory) and another in natural conditions. All organs of A. purpuratus depurated the toxin very quickly in both experiments. In some organs, an increase or a very small decrease of toxin was detected in the early depuration steps. Several models were used to describe this kinetics. The one that included toxin transfer between organs and independent depuration from each organ was the model that best fit the data. It seems, therefore, that the DA in this species is quickly transferred from the digestive gland to all other organs, which release it into the environment. Physiological differences in the two experiments have been shown to have some effect on the depuration from each organ but the actual reasons are still unknown.
| S-EPMC7692689 | biostudies-literature