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

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

Ectothermic species like fishes differ greatly in the thermal ranges they tolerate; some eurythermal species may encounter temperature ranges in excess of 25°C, whereas stenothermal species in polar and tropical waters live at essentially constant temperatures. Thermal specialization comes with fitness trade-offs and as temperature increases due to global warming, the physiological basis of specialization and thermal plasticity has become of great interest. Over the past 50 years, comparative physiologists have studied the physiological and molecular differences between stenothermal and eurythermal fishes. It is now well known that many stenothermal fishes have lost an inducible heat shock response (HSR). Recent advances in transcriptomics have now made it possible to examine genome-wide changes in gene expression (GE) in non-model ecologically important fish, broadening our view beyond the HSR to regulation of genes involved in hundreds of other cellular processes. Here, we review the major findings from transcriptomic studies of extreme eurythermal and stenothermal fishes in response to acute and long-term exposure to temperature, both time scales being critically important for predicting climate change responses. We consider possible molecular adaptations that underlie eurythermy and stenothermy in teleosts. Furthermore, we highlight the challenges that still face the field of comparative environmental genomics and suggest fruitful paths of future investigation.

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Transcriptomic responses to environmental temperature in eurythermal and stenothermal fishes

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

To understand the function of myoglobin (Mb) and cytoglobin (Cygb) in channel catfish Ictalurus punctatus in response to heat stress, mb and cygb genes were identified and characterized in this study. These genes were widely expressed in all the tested tissues, but strong tissue preferences were observed, with the mb gene being expressed most highly in the heart, cygb1 most highly expressed in the intestine and cygb2 most highly expressed in the brain. After heat-stress challenge, mb and cygb genes were up-regulated in almost all tested tissues. In general, such up-regulation was more dramatic in the tolerant group than in the intolerant group, suggesting that higher expression of mb and cygb genes contributed to greater tolerance of I. punctatus to heat stress.

Molecular characterization, phylogenetic analysis and expression profiling of myoglobin and cytoglobin genes in response to heat stress in channel catfish Ictalurus punctatus.

We report a case of adult-onset dystonia presenting with chronic progressive external ophthalmoplegia. The patient had ptosis in both eyes, particularly the left eye, for no obvious reason since the age of 10, which was progressively aggravated. The clinical diagnosis was chronic progressive external ophthalmoplegia. However, whole gene sequencing revealed the mitochondrial A3796G missense mutation, so the patient was clearly diagnosed as adult-onset dystonia and given treatment to reduce blood glucose and improve muscle metabolism. The A3796G mutation in the ND1 subunit of the mitochondrial complex leading to ophthalmoplegia is relatively rare, requiring a combination with genetic testing for confirmation of diagnosis.

J. R. Zhang

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

Molecular characterization, phylogenetic analysis and expression profiling of myoglobin and cytoglobin genes in response to heat stress in channel catfish Ictalurus punctatus.

[One case of adult-onset dystonia presenting with chronic progressive external ophthalmoplegia].