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      Domestication drive the changes of immune and digestive system of Eurasian perch ( Perca fluviatilis)

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          Abstract

          Domestication has altered a variety of traits within the Eurasian perch ( Perca fluviatilis), including phenotypic, physiological and behavioral traits of Eurasian perch ( Perca fluviatilis). Little is known, however, about the genetic changes between domesticated and wild Eurasian perch. In this study, we assembled a high-quality de novo reference transcriptome and identified differentially expressed genes between wild and domesticated Eurasian perch. A total of 113,709 transcripts were assembled, and 58,380 transcripts were annotated. Transcriptomic comparison revealed 630 differentially expressed genes between domesticated and wild Eurasian perch. Within domesticated Eurasian perch there were 412 genes that were up-regulated including MHCI, MHCII, chia, ighm within immune system development. There were 218 genes including try1, ctrl, ctrb, cela3b, cpa1 and cpb1, which were down-regulated that were associated with digestive processes. Our results indicated domestication drives the changes of immune and digestive system of Eurasian perch. Our study not only provide valuable genetic resources for further studies in Eurasian perch, but also provide novel insights into the genetic basis of physiological changes in Eurasian perch during domestication process.

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          Most cited references 40

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          The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

          The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.
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            Evo-devo and the evolution of social behavior.

            The integration of evolutionary biology with developmental genetics into the hybrid field of 'evo-devo' resulted in major advances in understanding multicellular development and morphological evolution. Here we show how insights from evo-devo can be applied to study the evolution of social behavior. We develop this idea by reviewing studies that suggest that molecular pathways controlling feeding behavior and reproduction in solitary insects are part of a 'genetic toolkit' underlying the evolution of a particularly complex form of social behavior, division of labor among workers in honeybee colonies. The evo-devo approach, coupled with advances in genomics for non-model genetic organisms, including the recent sequencing of the honeybee genome, promises to advance our understanding of the evolution of social behavior.
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              A population genetics view of animal domestication.

              The fundamental shift associated with the domestication of plants and animals allowed for a dramatic increase in human population sizes and the emergence of modern society. Despite its importance and the decades of research devoted to studying it, questions regarding the origins and processes of domestication remain. Here, we review recent theoretical advances and present a perspective that underscores the crucial role that population admixture has played in influencing the genomes of domestic animals over the past 10000 years. We then discuss novel approaches to generating and analysing genetic data, emphasising the importance of an explicit hypothesis-testing approach for the inference of the origins and subsequent evolution and demography of domestic animals. By applying next-generation sequencing technology alongside appropriate biostatistical methodologies, a substantially deeper understanding of domestication is on the horizon. Copyright © 2013 Elsevier Ltd. All rights reserved.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 March 2017
                2017
                : 12
                : 3
                Affiliations
                [1 ]Key Laboratory of Freshwater Fisheries Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
                [2 ]Fisheries Technology Extension Station, Xinjiang Production and Construction Corps, Urumqi, Xinjiang, China
                [3 ]Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
                Xiamen University, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: CHW ZHF XWC JW.

                • Data curation: JW XWC.

                • Formal analysis: JW XWC.

                • Investigation: ZHF LQ WX TA.

                • Writing – original draft: XWC.

                • Writing – review & editing: XWC JW CHW SG.

                Article
                PONE-D-16-44331
                10.1371/journal.pone.0172903
                5336236
                28257494
                aaf64db9-8400-493d-9076-a83432a0e1d2
                © 2017 Chen et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Page count
                Figures: 5, Tables: 2, Pages: 15
                Product
                Funding
                Funded by: National Key Technology Support Program
                Award ID: 2012BAD25B10-03
                Award Recipient :
                Funded by: Shanghai collaborative Innovation Center for Aquatic Animal Genetics and Breeding Project
                Award ID: ZF1206
                Award Recipient :
                Funded by: Shanghai Ocean University funding
                Award ID: A2-0203-00-100220
                Award Recipient :
                Funded by: National Science Foundation East Asia and Pacific Summer Institutes for U.S. Graduate Student
                Award ID: 1613917
                Award Recipient :
                This work was supported by the National Key Technology Support Program (Grant No.2012BAD25B10-03), the Shanghai collaborative Innovation Center for Aquatic Animal Genetics and Breeding Project (ZF1206), Shanghai Ocean University funding (Grant no A2- 0203-00-100220), and National Science Foundation East Asia and Pacific Summer Institutes for U.S. Graduate Students (1613917).
                Categories
                Research Article
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Organisms
                Animals
                Animal Types
                Domestic Animals
                Biology and Life Sciences
                Zoology
                Animal Types
                Domestic Animals
                Biology and Life Sciences
                Immunology
                Immune System Proteins
                Medicine and Health Sciences
                Immunology
                Immune System Proteins
                Biology and Life Sciences
                Biochemistry
                Proteins
                Immune System Proteins
                Biology and Life Sciences
                Immunology
                Immune Response
                Medicine and Health Sciences
                Immunology
                Immune Response
                Biology and Life Sciences
                Genetics
                Gene Expression
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Sequence Databases
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Databases
                Research and analysis methods
                Extraction techniques
                RNA extraction
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Sequencing techniques
                RNA sequencing
                Research and analysis methods
                Molecular biology techniques
                Sequencing techniques
                RNA sequencing
                Custom metadata
                Sequencing reads are available at NCBI SRA database (SRX2317605).

                Uncategorized

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