The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

Morris, Katrina M.; Hindle, Matthew; Boitard, Simon; Burt, David W.; Danner, Angela; Eöry, Lél; Forrest, H. S.; Gourichon, David; Gros, Jérôme; Gourichon, Lionel; Hillier, LaDeana W.; Jaffredo, Thierry; Khoury, Hanane; Leterrier, Christine; Loudon, A. S. I.; Mason, AS; Meddle, Simone; Minvielle, Francis; Minx, Patrick; Pitel, Frédérique; Seiler, J.; Shimmura, Tsuyoshi; Tomlinson, Chad; Vignal, Alain; Webster, Robert G.; Yoshimura, Takashi; Warren, Wes; Smith, Jacqueline

doi:10.1101/575332

Cited by 5 publications

(2 citation statements)

References 109 publications

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“…Sequence reads were aligned with BWA-MEM [21] to the Coturnix japonica 2.0 quail reference genome (NCBI assembly accession GCA_001577835.1; BioProject accession PRJNA314147), which consists of 32 chromosomes or linkage groups and 1095 un-localised scaffolds [22]. We used the Integrative Genome Viewer (IGV) software http://software.broadinstitute.org/software/igv/ to visualize the alignment on the reference genome and to check for compatibility of distance and orientation between read-pairs with the size selection that was set for the construction of the libraries.…”

Section: Methodsmentioning

confidence: 99%

Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail

et al. 2019

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Background In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the yellow mutation (large deletion) and the fawn -2/ beige mutation (assumed to be caused by a different structural modification). Results For the yellow phenotype, we identified a complex mutation that involves a 141,162-bp long deletion. For the fawn-2/beige phenotype, we identified a 71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH - ASIP fusion gene, which leads to a transcript coding for a normal ASIP protein. Although this agrees with previous reports that reported an increased level of ASIP transcripts in the skin of mutant animals, we show that in the skin from fawn-2/beige embryos, this level is higher than expected with a simple duplication of the ASIP gene. Thus, we hypothesize that the 5′ region of the ITCH - ASIP fusion gene leads to a higher transcription level than the 5′ region of the ASIP gene. Conclusions We were able to conclude that the fawn-2 and beige phenotypes are caused by the same allele at the ASIP locus. Both of the associated mutations fawn - 2/beige and yellow lead to the formation of a fusion gene, which encodes a transcript for the ASIP protein. In both cases, transcription of ASIP depends on the promoter of a different gene, which includes alternative up-regulating sequences. However, we cannot exclude the possibility that the loss of the 5′ region of the ASIP gene itself has additional impacts, especially for the fawn - 2/beige mutation. In addition, in several other species including mammals, the existence of other dominant gain-of-function structural modifications that are localized upstream of the ASIP coding sequences has been reported, which supports our hypothesis that repressors in the 5′ region of ASIP are absent in the fawn -2/ beige mutant. Electronic supplementary material The online version of this article (10.1186/s12711-019-0458-6) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail

et al. 2019

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“…Immune system-related research in birds is crucial to better understand, for instance, the spread of zoonotic diseases which is not only important in the context of species conservation but also has a potentially great impact on human health and economy (livestock). Birds are highly mobile with some migrating long distances and are thus a potential reservoir and vector for zoonotic diseases [23][24][25][26][27]. Therefore, eco-immunology [28,29] has gained momentum over the last decade [21,30,31].…”

Section: Introductionmentioning

confidence: 99%

Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

et al. 2020

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Background Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the “correct” set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K (“Bird 10,000 Genomes”) consortium’s whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm. Construction and content A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the “seed” for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database. Utility and discussion The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.

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Avian Genomics in Animal Breeding and the End of the Model Organism

Vignal

Eöry

2019

Avian Genomics in Ecology and Evolution

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The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

Cited by 5 publications

References 109 publications

Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail

Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail

Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

Avian Genomics in Animal Breeding and the End of the Model Organism

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