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      Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities

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          Abstract

          Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome–environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcriptome assemblies that provide a valuable resource for studies of genome evolution (e.g. polyploidy), ecological and morphological diversification, speciation, and shared and unique responses to environmental variation in cyprinid fishes. Our results and analyses address the following points: (i) ‘essential developmental genes’ are shown to be ubiquitously expressed in a diverse suite of tissues across later ontogenetic stages (i.e. juveniles and adults), making these genes are useful for assessing the quality of transcriptome assemblies, (ii) the influence of microbiomes and other exogenous DNA, (iii) potentially novel, species-specific genes, and (iv) genomic rearrangements (e.g. whole genome duplication). The data we present provide a resource for future comparative work in cypriniform fishes and other taxa across a variety of sub-disciplines, including stress response, morphological diversification, community ecology, ecotoxicology, and climate change.

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          The impact of next-generation sequencing technology on genetics.

          If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism.
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            Next-generation transcriptome assembly.

            Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.
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              Applications of next generation sequencing in molecular ecology of non-model organisms.

              As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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                Author and article information

                Journal
                DNA Res
                DNA Res
                dnares
                DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
                Oxford University Press
                1340-2838
                1756-1663
                February 2018
                06 September 2017
                06 September 2017
                : 25
                : 1
                : 11-23
                Affiliations
                Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
                Author notes
                To whom correspondence should be addressed. Tel. 716-645-2363. Fax. 716-645-2975. Email: krabbent.j@ 123456gmail.com

                Present address: Department of Biological Sciences and Research and Education in eNergy, Environment and Water Program (RENEW), University at Buffalo, Buffalo, NY 14260-1300, USA Edited by Prof. Masahira Hattori

                Article
                dsx034
                10.1093/dnares/dsx034
                5824830
                28985264
                9b12f39d-6904-4935-a999-09cb27667118
                © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                Page count
                Pages: 13
                Product
                Funding
                Funded by: National Institute of General Medical Sciences 10.13039/100000057
                Award ID: 8P20GM103451-12
                Categories
                Full Papers

                Genetics
                rna-seq,essential genes,cyprinus carpio,carp,gene silencing
                Genetics
                rna-seq, essential genes, cyprinus carpio, carp, gene silencing

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