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Gallus gallus isolate:RJF #256 | breed:Red Jungle fowl

ABSTRACT: The Chicken Genome Project, currently maintained by the Genome Reference Consortium (GRC)

PROVIDER: PRJNA13342 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR000635.fastq.gz	Fastqsanger.gz
	SRR000636.fastq.gz	Fastqsanger.gz
	SRR000637.fastq.gz	Fastqsanger.gz
	SRR000638.fastq.gz	Fastqsanger.gz

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Gallus gallus strain:silky fowl chicken | isolate:BB | breed:Black-bone chicken

Project description:Gallus gallus strain:silky fowl chicken | isolate:BB | breed:Black-bone chicken Raw sequence reads

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Gallus gallus breed:Isabrown

Project description:Chicken egg protein

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Hyperpigmentation Results in Aberrant Immune Development in Silky Fowl (Gallus gallus domesticus Brisson).

Project description:The Silky Fowl (SF) is known for its special phenotypes and atypical distribution of melanocytes among internal organs. Although the genes associated with melanocyte migration have been investigated substantially, there is little information on the postnatal distribution of melanocytes in inner organs and the effect of hyperpigmentation on the development of SF. Here, we analyzed melanocyte distribution in 26 tissues or organs on postnatal day 1 and weeks 2, 3, 4, 6, 10, and 23. Except for the liver, pancreas, pituitary gland, and adrenal gland, melanocytes were distributed throughout the body, primarily around blood vessels. Interaction between melanocytes and the tissue cells was observed, and melanin was transported by filopodia delivery through engulfed and internalized membrane-encapsulated melanosomes. SFs less than 10 weeks old have lower indices of spleen, thymus, and bursa of Fabricius than White Leghorns (WLs). The expression levels of interferon-γ and interlukin-4 genes in the spleen, and serum antibody levels against H5N1 and infectious bursal disease virus were lower in SF than in WL. We also found immune organ developmental difference between Black-boned and non-Black- boned chickens from SFs and WLs hybrid F2 population. However, degeneration of the thymus and bursa of Fabricius occurred later in SF than in WL after sexual maturity. Analysis of apoptotic cells and apoptosis-associated Bax and Bcl-2 proteins indicated that apoptosis is involved in degeneration of the thymus and bursa of Fabricius. Therefore, these results suggest that hyperpigmentation in SF may have a close relationship with immune development in SF, which can provide an important animal model to investigate the roles of melanocyte.

| S-EPMC4457905 | biostudies-literature

Gallus gallus breed:Ross 308

Project description:Chicken Metagenome

| PRJNA380214 | ENA

Gallus gallus breed:Gushi

Project description:chicken Raw sequence reads

| PRJNA380024 | ENA

Gallus gallus breed:Lohmann Brown

Project description:Chicken oocyte transcriptome

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Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools.

Project description:BackgroundThe program RepeatMasker and the database Repbase-ISB are part of the most widely used strategy for annotating repeats in animal genomes. They have been used to show that avian genomes have a lower repeat content (8-12 %) than the sequenced genomes of many vertebrate species (30-55 %). However, the efficiency of such a library-based strategies is dependent on the quality and completeness of the sequences in the database that is used. An alternative to these library based methods are methods that identify repeats de novo. These alternative methods have existed for a least a decade and may be more powerful than the library based methods. We have used an annotation strategy involving several complementary de novo tools to determine the repeat content of the model genome galGal4 (1.04 Gbp), including identifying simple sequence repeats (SSRs), tandem repeats and transposable elements (TEs).ResultsWe annotated over one Gbp. of the galGal4 genome and showed that it is composed of approximately 19 % SSRs and TEs repeats. Furthermore, we estimate that the actual genome of the red jungle fowl contains about 31-35 % repeats. We find that library-based methods tend to overestimate TE diversity. These results have a major impact on the current understanding of repeats distributions throughout chromosomes in the red jungle fowl.ConclusionsOur results are a proof of concept of the reliability of using de novo tools to annotate repeats in large animal genomes. They have also revealed issues that will need to be resolved in order to develop gold-standard methodologies for annotating repeats in eukaryote genomes.

| S-EPMC4992247 | biostudies-literature

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