KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.

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RNA-Seq technology and its application in fish transcriptomics.

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries. Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

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Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

The zebrafish (Danio rerio) is a freshwater teleost of the family Cyprinidae that is established as a model organism in many research fields. Here, we define the characteristics that a fish species should have to serve as a model for finfish aquaculture research and argue that the zebrafish fulfils essentially most of them. We first describe several aspects of the biology of the zebrafish including phylogenetic relationships, development and growth and reproduction, both in the wild and under laboratory conditions. Next, we review the work already carried out in zebrafish that is related to different aspects of aquaculture research (reproduction, stress, pathology, toxicology nutrition and growth). We assess critically the areas in which zebrafish still offers further potential as a model organism for aquaculture, which include, but are not limited to, development, immunology, genomics and reproduction. In other areas, however, limitations must be borne in mind and caution must be taken when extrapolating results. This is, for example, the case of some growth studies. Finally, we provide information on resources for research with zebrafish. Current general limitations of work with zebrafish come from the fact that in contrast to other laboratory animal models such as rodents, strict breeding protocols are generally not adopted. Nevertheless, as there is no major obstacle to overcome these limitations and due to its intrinsic advantages, we conclude that the zebrafish is likely to play an increasing role as a model organism in many areas of research for finfish aquaculture.

The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research

Wild populations increasingly experience extreme conditions as climate change amplifies environmental variability. How individuals respond to environmental extremes determines the impact of climate change overall. The variability of response from individual to individual can represent the opportunity for natural selection to occur as a result of extreme conditions. Here, we experimentally replicated the natural exposure to extreme temperatures of the reef lagoon at Ofu Island (American Samoa), where corals can experience severe heat stress during midday low tide. We investigated the bleaching and transcriptome response of 20 Acropora hyacinthus colonies 5 and 20 h after exposure to control (29 °C) or heated (35 °C) conditions. We found a highly dynamic transcriptome response: 27% of the coral transcriptome was significantly regulated 1 h postheat exposure. Yet 15 h later, when heat-induced coral bleaching became apparent, only 12% of the transcriptome was differentially regulated. A large proportion of responsive genes at the first time point returned to control levels, others remained differentially expressed over time, while an entirely different subset of genes was successively regulated at the second time point. However, a noteworthy variability in gene expression was observed among individual coral colonies. Among the genes of which expression lingered over time, fast return to normal levels was associated with low bleaching. Colonies that maintained higher expression levels of these genes bleached severely. Return to normal levels of gene expression after stress has been termed transcriptome resilience, and in the case of some specific genes may signal the physiological health and response ability of individuals to environmental stress.

The role of transcriptome resilience in resistance of corals to bleaching

Shikai Liu,* Xiuli Wang,* Fanyue Sun, Jiaren Zhang, Jianbin Feng, Hong Liu, K. V. Rajendran, Luyang Sun, Yu Zhang, Yanliang Jiang, Eric Peatman, Ludmilla Kaltenboeck, Huseyin Kucuktas, and Zhanjiang Liu The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama; The Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, Peoples Republic of China; and College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning, Peoples Republic of China

CALL FOR PAPERS NextGen Sequencing Technology-based Dissection of Physiological Systems RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org.

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1142&context=ans_pubs

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

degradation in response to heat stress in catfish in oxygen transport, protein synthesis, folding, and RNA-Seq reveals expression signatures of genes involved

The lectin pathway of the complement system is characterized by two groups of soluble pattern recognition molecules, mannose-binding lectins (MBLs) and ficolins. These molecules recognize and bind carbohydrates in pathogens and activate complement leading to opsonization, leukocyte activation, and direct pathogen killing. While MBLs have been reported in many fish species, ficolins do not appear to be present in the teleost lineage, despite their importance in invertebrate and higher vertebrate innate immunity. A protein with a similar fibrinogen-like domain, microfibrillar-associated protein 4, MFAP4, is present in fish, albeit with no described immune function. We examined whether MFAP4 genes in fish may potentially act as pathogen receptors in the absence of ficolin. We isolated and characterized five MFAP4 genes from channel catfish. Linkage mapping and phylogenetic analysis indicated that at least three of the catfish MFAP4 genes are tightly clustered on a single chromosome, suggesting that they may have arisen through tandem duplication. Divergent, duplicated families of MFAP4 genes are also present in other teleost species. Expression analysis of the catfish MFAP4 transcripts revealed unique patterns of homeostatic expression among the genes in gill, spleen, skin, liver, and muscle. Expression of the five MFAP4 transcripts showed significant changes in expression as soon as 4 h after infection with either Edwardsiella ictaluri or Flavobacterium columnare with modulation of expression continuing up to 7 d following pathogen exposure. Several different tissues and gene-specific patterns were captured and transcript expression changes of >30-fold were observed over the course of the bacterial challenges. Our results suggest a novel role for MFAP4 in teleost immune responses.

Eric Peatman

Papers

CALL FOR PAPERS NextGen Sequencing Technology-based Dissection of Physiological Systems RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

degradation in response to heat stress in catfish in oxygen transport, protein synthesis, folding, and RNA-Seq reveals expression signatures of genes involved

Developmental and Comparative Immunology