Isolation and characterization of microsatellite markers in a highland fish, Pareuchiloglanis sinensis (Siluriformes: Sisoridae) by next-generation sequencing

Chen, Weitao; He, Shunping

doi:10.1007/s12041-018-0997-6

Cited by 4 publications

(1 citation statement)

References 9 publications

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“…OMICs require high-throughput technologies and each different OMIC uses a specific set of analytical technologies. For instance, transcriptomics was first based on the use of arrays [ 23 ] and later evolved into the use of next generation sequencing (NGS) of DNA and RNA [ 24 , 25 ]. Similarly, proteomics that was first based on two-dimensional gel electrophoresis with protein identification using mass spectrometry (MS) later evolved into gel-free techniques able to quantitate large numbers of proteins using MS. For instance, high-throughput LC-MS/MS, combined with isotope-coded affinity tags (ICAT) labelling and peptide enrichment, enabled to describe proteomic alterations related with phosphorylation and OA inhibition of PP2A and PP1 [ 26 ].…”

Section: Omics Overviewmentioning

confidence: 99%

OMICs Approaches in Diarrhetic Shellfish Toxins Research

Campos

Freitas

Almeida

et al. 2020

Toxins

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Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe’s and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms’ metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.

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Section: Omics Overviewmentioning

confidence: 99%

OMICs Approaches in Diarrhetic Shellfish Toxins Research

Campos

Freitas

Almeida

et al. 2020

Toxins

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De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Ding

Kumpeangkeaw

et al. 2019

Physiol Mol Biol Plants

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Lemna gibba is a species of duckweed showing great potential in bioenergy production and wastewater treatment. However, the relevant transcriptomic and genomic resources are very limited for this species, which dramatically hinders its genetic diversity and genome mapping researches. In this work, * 233.5 million clean reads were generated from L. gibba by Illumina paired-end sequencing, and subsequently they were de novo assembled into 131,870 unigenes, of which 61,622 were annotated and 43,319 were expressed with Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) [ 5. In total, 19,297 simple sequence repeats (SSRs) were identified from 15,261 SSR-containing unigenes. Dinucleotide (78.4%) were the most abundant SSRs, followed by tri-(14.9%), tetra-(4.1%), and penta-nucleotides (1.5%). The top three motifs were AG/CT (69.9%), AC/GT (6.5%), and ATC/ATG (4.9%). Further analysis revealed that the presence of SSR motif was independent of the expression level for a given gene. Based on the sequence of these SSR-containing unigenes, a total of 10,292 SSR markers were developed, of which only 2671 were further retained after removing those derived from unannotated or extra-low expressed (e.g., FPKM B 5) unigenes. Finally, a subset of 70 SSR markers was randomly selected and examined in nine diverse L. gibba genotypes for the PCR amplification and polymorphism, as well as in other duckweed species for the inter-specifically amplifiability. This work is the first report on the transcriptome-based large-scale SSR markers development and analysis in L. gibba. The transcriptome generated and the SSR markers developed in this work will provide a valuable resource for genetic diversity assessment in L. gibba and also for species relationship investigation in Lemnaceae family.Lili Fu and Zehong Ding have contributed equally to this work.

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Discrimination of Moutan Cortex from different sources and geographical origins for quality evaluation using microsatellite markers coupled with chemical analysis

Zhang

Wang

et al. 2020

Biochemical Systematics and Ecology

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Isolation and characterization of microsatellite markers in a highland fish, Pareuchiloglanis sinensis (Siluriformes: Sisoridae) by next-generation sequencing

Cited by 4 publications

References 9 publications

OMICs Approaches in Diarrhetic Shellfish Toxins Research

OMICs Approaches in Diarrhetic Shellfish Toxins Research

De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba

Discrimination of Moutan Cortex from different sources and geographical origins for quality evaluation using microsatellite markers coupled with chemical analysis

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