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High-Throughput Sequencing Data Analysis for Industrial Applications
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High-Throughput Sequencing Data Analysis for Industrial Applications

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 6334

Special Issue Editors

Dr. Kakeru Yokoi

E-Mail Website
Guest Editor
Institute of Agrobiological Sciences, NARO, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
Interests: entomology; bioinformatics; genome data analysis; trancriptomics; molecular biology; immunology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Hidemasa Bono

E-Mail Website
Guest Editor
Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-0046, Japan
Interests: bioinformatics; biological databases; genome editing; genome sequencing; sequence analysis; transcriptome analysis; functional genomics; hypoxia; oxidative stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent high-throughput DNA sequencers have made it possible to generate DNA and RNA sequence data at a low cost and in a short time. They revolutionized biological research. For instance, high-quality genome sequence data or transcriptome data including many samples of model and non-model species, such as insects, fishes and plants, have been available, or the compositions of microorganisms in multiple environments can be revealed (meta-genome analysis). In the future, modified biological resources are expected to be designed by the combination of the analysis of high-throughput nucleotide data and gene modification techniques. This Special Issue will provide an overview of the latest applications of data analysis to biological research, with a main focus on the bio-industries. The aim of this Special Issue is to promote biological research using sequence data analysis for the industrial utilization of new biological resources. Authors are requested to deposit newly sequenced data and to include the accession IDs of the data in the manuscript. Additionally, the analyzed data files (e.g., the expression value table of all transcripts) should be uploaded to public data repositories such as figshare, and the DOI (Digital Object Identifier) of the data should be displayed to ensure the reproducibility of data analysis. Potential topics include, but are not limited to:

  • Biological mechanisms at the molecular or genetic level using a non-human model;
  • Reference genome and transcriptome data for industry-important model and non-model organisms;
  • Ecological reports using high-throughput sequence data;
  • Metagenomics in model and non-model organisms and its application to industry;
  • Meta-analysis using high-throughput sequence data deposited in a public database (NCBI/ENA/DDBJ);
  • Genome editing research for industrial applications using high-throughput sequencing in model and non-model organisms.

Dr. Kakeru Yokoi
Prof. Dr. Hidemasa Bono
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • next-generation sequencer (NGS)
  • meta-analysis
  • genome analysis
  • transcriptome analysis
  • metagenome analysis
  • genome editing

Published Papers (4 papers)

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Research

14 pages, 1977 KiB  
Article
The Development of New Methods to Stimulate the Production of Antimicrobial Peptides in the Larvae of the Black Soldier Fly Hermetia illucens
by Atsuyoshi Nakagawa, Takuma Sakamoto, Michael R. Kanost and Hiroko Tabunoki
Int. J. Mol. Sci. 2023, 24(21), 15765; https://doi.org/10.3390/ijms242115765 - 30 Oct 2023
Viewed by 1029
Abstract
(1) The global population is projected to reach a staggering 9.8 billion people by the year 2050, leading to major concerns about food security. The necessity to increase livestock production is inevitable. The black soldier fly (BSF) is known for its ability to [...] Read more.
(1) The global population is projected to reach a staggering 9.8 billion people by the year 2050, leading to major concerns about food security. The necessity to increase livestock production is inevitable. The black soldier fly (BSF) is known for its ability to consume a wide range of organic waste, and BSF larvae have already been used as a partial substitute for fishmeal. In contrast, the use of antibiotics in livestock feed for growth promotion and prophylaxis poses a severe threat to global health owing to antimicrobial resistance. Insect antimicrobial peptides (AMPs) have shown the potential to rapidly disrupt target bacterial membranes, making bacterial resistance to AMPs a less likely concern. (2) In this study, we explored various methods for stimulating AMP synthesis in BSF larvae and found that thermal injury effectively induced the production of various AMP types. Additionally, we investigated the activation of innate immune response pathways that lead to AMP production following thermal injury. (3) Interestingly, thermal injury treatment, although not involving bacteria, exhibited a similar response to that observed following Gram-positive bacterial infection in eliciting the expression of AMP genes. (4) Our findings offer support for the industrial use of BSF to enhance livestock production and promote environmental health. Full article
(This article belongs to the Special Issue High-Throughput Sequencing Data Analysis for Industrial Applications)
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16 pages, 5462 KiB  
Article
Meta-Analysis of Heat-Stressed Transcriptomes Using the Public Gene Expression Database from Human and Mouse Samples
by Sora Yonezawa and Hidemasa Bono
Int. J. Mol. Sci. 2023, 24(17), 13444; https://doi.org/10.3390/ijms241713444 - 30 Aug 2023
Viewed by 1657
Abstract
Climate change has significantly increased the frequency of our exposure to heat, adversely affecting human health and industries. Heat stress is an environmental stress defined as the exposure of organisms and cells to abnormally high temperatures. To comprehensively explain the mechanisms underlying an [...] Read more.
Climate change has significantly increased the frequency of our exposure to heat, adversely affecting human health and industries. Heat stress is an environmental stress defined as the exposure of organisms and cells to abnormally high temperatures. To comprehensively explain the mechanisms underlying an organism’s response to heat stress, it is essential to investigate and analyze genes that have been under-represented or less well-known in previous studies. In this study, we analyzed heat stress-responsive genes using a meta-analysis of numerous gene expression datasets from the public database. We obtained 322 human and 242 mouse pairs as the heat exposure and control data. The meta-analysis of these data identified 76 upregulated and 37 downregulated genes common to both humans and mice. We performed enrichment, protein–protein interaction network, and transcription factor target gene analyses for these genes. Furthermore, we conducted an integrated analysis of these genes using publicly available chromatin immunoprecipitation sequencing (ChIP-seq) data for HSF1, HSF2, and PPARGC1A (PGC-1α) as well as gene2pubmed data from the existing literature. The results identified previously overlooked genes, such as ABHD3, ZFAND2A, and USPL1, as commonly upregulated genes. Further functional analysis of these genes can contribute to coping with climate change and potentially lead to technological advancements. Full article
(This article belongs to the Special Issue High-Throughput Sequencing Data Analysis for Industrial Applications)
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18 pages, 8847 KiB  
Article
Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae)
by Yantao Liu, Tianwei Liu, Yuzhen Wang, Jing Liu, Bingjian Liu, Li Gong, Zhenming Lü and Liqin Liu
Int. J. Mol. Sci. 2023, 24(16), 12892; https://doi.org/10.3390/ijms241612892 - 17 Aug 2023
Cited by 1 | Viewed by 1241
Abstract
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the [...] Read more.
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts. Full article
(This article belongs to the Special Issue High-Throughput Sequencing Data Analysis for Industrial Applications)
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14 pages, 2031 KiB  
Article
Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites
by Kouhei Toga and Hidemasa Bono
Int. J. Mol. Sci. 2023, 24(9), 8353; https://doi.org/10.3390/ijms24098353 - 6 May 2023
Cited by 1 | Viewed by 1888
Abstract
Eusociality in insects has evolved independently many times. One of the most notable characteristics of eusociality is the reproductive division of labor. In social insects, the reproductive division of labor is accomplished by queens and workers. Transcriptome analyses of queens and workers have [...] Read more.
Eusociality in insects has evolved independently many times. One of the most notable characteristics of eusociality is the reproductive division of labor. In social insects, the reproductive division of labor is accomplished by queens and workers. Transcriptome analyses of queens and workers have been conducted for various eusocial species. However, the genes that regulate the reproductive division of labor across all or multiple eusocial species have not yet been fully elucidated. Therefore, we conducted a meta-analysis using publicly available RNA-sequencing data from four major groups of social insects. In this meta-analysis, we collected 258 pairs (queen vs. worker) of RNA-sequencing data from 34 eusocial species. The meta-analysis identified a total of 20 genes that were differentially expressed in queens or workers. Out of these, 12 genes have not previously been reported to be involved in the reproductive division of labor. Functional annotation of these 20 genes in other organisms revealed that they could be regulators of behaviors and physiological states related to the reproductive division of labor. These 20 genes, revealed using massive datasets of numerous eusocial insects, may be key regulators of the reproductive division of labor. Full article
(This article belongs to the Special Issue High-Throughput Sequencing Data Analysis for Industrial Applications)
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