Pagothenia borchgrevinki
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA183674 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR764594.fastq.gz | Fastqsanger.gz | |||
| SRR765754.fastq.gz | Fastqsanger.gz |
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Project description:Pagothenia borchgrevinki Transcriptome or Gene expression
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Project description:Transcriptional response of Pagothenia borchgrevinki during warm acclimation to 4°C
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Project description:Pagothenia borchgrevinki isolate:AGRC-2024 Genome sequencing
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Project description:Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki
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Project description:Antarctic icefish Pagothenia borchgrevinki is an ideal model for studying heat stress mechanisms. The complete mitochondrial genome of P. borchgrevinki was sequenced in this study. The genome sequence is 17,299 bp in length, which comprises 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a control region. The overall base composition is 20.45% G, 25.11% A, 29.46% T and 24.98 C%, with an A:T content of 54.57%.
| S-EPMC7799754 | biostudies-literature
Project description:BackgroundAmong the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of the Southern Ocean. Because P. borchgrevinki is a frequent model for investigating notothenioid cold-adaptation and specialization, it is imperative that "omic" tools be developed for this species. In the absence of a sequenced genome, a well annotated reference transcriptome of the bald notothen will serve as a model of gene expression in the coldest and harshest of all polar marine environments, useful for future comparative studies of cold adaptation and thermal responses in polar teleosts and ectotherms.ResultsWe sequenced and annotated a reference transcriptome for P. borchgrevinki, with added attention to capturing the transcriptional responses to acute and chronic heat exposures. We sequenced by Roche 454 a normalized cDNA library constructed from pooled mRNA encompassing multiple tissues taken from environmental, warm acclimating, and acute heat stressed specimens. The resulting reads were assembled into 42,620 contigs, 17,951 of which could be annotated. We utilized this annotated portion of the reference transcriptome to map short Illumina reads sequenced from the gill and liver of environmental specimens, and also compared the gene expression profiles of these two tissue transcriptomes with those from the temperate model fish Danio rerio. From this, we identified a conserved group of 58 GO terms, in which terms related to transcription and its regulation, ubiquitin-protein ligase activity, protein ubiquitination, and protein binding among others are more prevalent in the bald notothen, suggesting the pertinent genes play essential roles in cold temperature functioning.ConclusionWe sequenced multiple tissue transcriptomes from native and heat-exposed experimental specimens of the high Antarctic, cryopelagic notothenioid P. borchgrevinki to construct a reference transcriptome. In a proof of concept, we utilized the annotated reference transcriptome to profile the gene expression patterns of gill and liver, and identified a suite of over and under-represented GO terms when compared to the tropical water zebrafish suggesting these functions may be important for surviving in freezing waters. The transcriptome resource from this study will aid future investigations of cold adaptation and thermal response of polar ectothermic species.
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Project description:For any genome-based research, a robust genome assembly is required. De novo assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least 3 phases: (1) short-read only, (2) short- and long-read hybrid, and (3) long-read only assemblies. Each of the phases has its own error model. We hypothesized that hidden short-read scaffolding errors and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of Trematomus borchgrevinki from data generated during each of the 3 phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-mer-based strategy improved short-read assemblies as measured by Benchmarking Universal Single-Copy Ortholog while mate-pair libraries introduced hidden scaffolding errors and perturbed Benchmarking Universal Single-Copy Ortholog scores. Furthermore, we found that although hybrid assemblies can generate higher contiguity they tend to suffer from lower quality. In addition, we found long-read-only assemblies can be optimized for contiguity by subsampling length-restricted raw reads. Our results indicate that long-read contig assembly is the current best choice and that assemblies from phase I and phase II were of lower quality.
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Project description:Many bivalve species produce groups of strong proteinaceous byssal threads to rigidly attach to underwater substrates. Fibres like these have potential applications as biomedical materials due to their unique mechanical characteristics. The byssus and byssal thread producing glands of Pinctada maxima have not yet been characterised. RNA was isolated from P. maxima foot and byssal stem region tissues and sequenced using the Illumina platform. A de novo reference transcriptome comprising 34,281 contiguous sequences was assembled, and tissue replicates were mapped against the reference for quantitative analysis. Tryptic digests of byssal threads were analysed by LC-MS/MS. The resultant peptides were matched to 62 protein sequences derived from our reference transcriptome. Components of the byssus were identified for further characterisation, including a highly expressed perlucin-like foot protein (Pmfp1) and a recently identified protein that we refer to herein as glycine-rich thread (GRT) protein. This work provides principal knowledge on the molecular components of the byssus for P. maxima and the foot ultrastructure involved in the creation of byssal threads. This study advances our knowledge of byssus biosynthesis in non-mytilids, providing a platform for the design of new marine biopolymers.
2022-07-31 | PXD028273 | Pride
Project description:The goal of this study was to produce a reference transcriptome for the nickel hyperaccumulator Leucocroton havanensis endemic from Cuba and use this transcriptome as a reference to identify genes responding to the presence or the absence of nickel in both roots and shoots of this species
2024-07-10 | GSE237255 | GEO