Characterization of Physa acuta expressed sequence tags and transcript mining following cadmium exposure

Jeong, Ji Eun; Patnaik, Bharat Bhusan; Kang, Se Won; Hwang, Hyeon‐Jong; Park, So Young; Wang, Tae Hun; Park, Eun Bi; Lee, Jae Bong; Nam, Myung-Mo; Jo, Yong Hun; Lee, Junsang; Park, Hong Seog

doi:10.1007/s13258-015-0334-x

Cited by 2 publications

(2 citation statements)

References 30 publications

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“…Hypoxia affects the transcription of genes or gene regions associated with oxygen-related proteins [77]. Through transcriptome exploration, it has been possible to shed light on new biomarkers by expressed sequence tags (ESTs) or via pilot bioassays for heavy metal environmental remediation and impact assessments, which have been conducted with the mollusk Physa acuta and the green alga Chlamydomonas reinhardtii [44,87]. Dietary aspects of invertebrates and meiofauna exposed to toxic algae have been reported through transcriptomics analysis to recognize the effect of genes and presumably biological pathways [71,88].…”

Section: Transcriptomicsmentioning

confidence: 99%

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Machuca-Sepúlveda

Miranda

Lefin

et al. 2023

Biology

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Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.

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Section: Transcriptomicsmentioning

confidence: 99%

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Machuca-Sepúlveda

Miranda

Lefin

et al. 2023

Biology

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“…From the NGS sequencing and assembly processes to the annotation analysis, many datasets in different file formats are shared within researchers that warrants an expansion in hard disk storage (Baker, 2010 we constructed a local stand-alone BLAST server for the mollusk by translating the downloaded DNA and amino acid sequences from NCBI using the formatdb program (Lee et al, 2004). The BLAST server was convenient for quick and contamination-free annotation of large-scale EST data generated through first-generation Sanger sequencers (Jeong et al, 2013;Jeong et al, 2015). Subsequently, we developed mollusks sequence database (an updated version of stand-alone BLAST server for the mollusk) (http://www.malacol.or.kr/blast) that suggested a modification of the server to improve the significant hits percentage during the annotation of molluscan genes (Kang et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks

Kang¹,

Park²,

Patnaik³

et al. 2015

The Korean Journal of Malacology

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A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groupsArthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.

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Characterization of Physa acuta expressed sequence tags and transcript mining following cadmium exposure

Cited by 2 publications

References 30 publications

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks

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