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      Oxytocin variation and brain region‐specific gene expression in a domesticated avian species

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          Abstract

          The Bengalese finch was domesticated more than 250 years ago from the wild white‐rumped munia (WRM). Similar to other domesticated species, Bengalese finches show a reduced fear response and have lower corticosterone levels, compared to WRMs. Bengalese finches and munias also have different song types. Since oxytocin ( OT) has been found to be involved in stress coping and auditory processing, we tested whether the OT sequence and brain expression pattern and content differ in wild munias and domesticated Bengalese finches. We sequenced the OT from 10 wild munias and 11 Bengalese finches and identified intra‐strain variability in both the untranslated and protein‐coding regions of the sequence, with all the latter giving rise to synonymous mutations. Several of these changes fall in specific transcription factor‐binding sites, and show either a conserved or a relaxed evolutionary trend in the avian lineage, and in vertebrates in general. Although in situ hybridization in several hypothalamic nuclei did not reveal significant differences in the number of cells expressing OT between the two strains, real‐time quantitative PCR showed a significantly higher OT mRNA expression in the cerebrum of the Bengalese finches relative to munias, but a significantly lower expression in their diencephalon. Our study thus points to a brain region‐specific pattern of neurochemical expression in domesticated and wild avian strains, which could be linked to domestication and the behavioral changes associated with it.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Towards complete and error-free genome assemblies of all vertebrate species

            High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1 – 4 . To address this issue, the international Genome 10K (G10K) consortium 5 , 6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences. The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights.
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              TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

              We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.
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                Author and article information

                Contributors
                tobari@azabu-u.ac.jp
                cokanoya@mail.ecc.u-tokyo.ac.jp
                Journal
                Genes Brain Behav
                Genes Brain Behav
                10.1111/(ISSN)1601-183X
                GBB
                Genes, Brain, and Behavior
                Blackwell Publishing Ltd (Oxford, UK )
                1601-1848
                1601-183X
                02 December 2021
                February 2022
                : 21
                : 2 ( doiID: 10.1111/gbb.v21.2 )
                : e12780
                Affiliations
                [ 1 ] Department of Animal Science and Biotechnology, School of Veterinary Medicine Azabu University Sagamihara Japan
                [ 2 ] Center for Human and Animal Symbiosis Science Azabu University Sagamihara Japan
                [ 3 ] Laboratory of Neurogenetics of Language Rockefeller University New York New York USA
                [ 4 ] Department of Life Sciences The University of Tokyo Meguro‐ku Japan
                [ 5 ] Department of Biological Science, Graduate School of Science and Engineering University of Toyama Toyama Japan
                [ 6 ] Faculty of Health Sciences Nihon Institute of Medical Science Moroyama Japan
                [ 7 ] Council of Agriculture Endemic Species Research Institute (ESRI) Chi‐chi Taiwan
                [ 8 ] Department of Animal Science National Chung Hsing University Taichung Taiwan
                [ 9 ] Section of General Linguistics University of Barcelona Barcelona Spain
                [ 10 ] Institute for Complex Systems Universitat de Barcelona Barcelona Spain
                [ 11 ] ICREA Barcelona Spain
                [ 12 ] Howard Hughes Medical Institute Chevy Chase Maryland USA
                [ 13 ] Cognition and Behavior Joint Laboratory RIKEN Center for Brain Science (Brain Science Institute (BSI) reorganized) Saitama Japan
                Author notes
                [*] [* ] Correspondence

                Yasuko Tobari, Department of Animal Science and Biotechnology, Azabu University, Fuchinobe 1‐17‐71, Chuo‐ku, Sagamihara 252‐5201, Japan.

                Email: tobari@ 123456azabu-u.ac.jp

                Kazuo Okanoya, Department of Life Sciences, The University of Tokyo, 3‐8‐1 Komaba, Meguro‐ku, Tokyo 153‐8902, Japan.

                Email: cokanoya@ 123456mail.ecc.u-tokyo.ac.jp

                Author information
                https://orcid.org/0000-0003-4438-2912
                Article
                GBB12780
                10.1111/gbb.12780
                9744569
                34854547
                36fc238d-1343-4ac4-9cc6-016e47e73d18
                © 2021 The Authors. Genes, Brain and Behavior published by International Behavioural and Neural Genetics Society and John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 07 November 2021
                : 18 March 2021
                : 09 November 2021
                Page count
                Figures: 8, Tables: 0, Pages: 15, Words: 12963
                Funding
                Funded by: Howard Hughes Medical Institute , doi 10.13039/100000011;
                Funded by: Ministry of Education, Culture, Sports, Science and Technology Japan
                Award ID: JP16K18585
                Award ID: JP19K06751
                Funded by: Moritani Scholarship Foundation , doi 10.13039/501100006684;
                Funded by: Rockefeller University , doi 10.13039/100012007;
                Funded by: Spanish Science Ministry
                Award ID: PID2019‐107042GB‐I00
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                February 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.1 mode:remove_FC converted:17.11.2022

                Neurosciences
                domestication,gene expression,inter‐strain difference,intra‐strain variability,mesotocin,oxytocin,songbird

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