Dataset Information

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.

ABSTRACT: The 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).We 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.Our 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.

SUBMITTER: Guizard S

PROVIDER: S-EPMC4992247 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Publications

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.

Guizard Sébastien S Piégu Benoît B Arensburger Peter P Guillou Florian F Bigot Yves Y

BMC genomics 20160819 1

<h4>Background</h4>The 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 metho ...[more]

PMID: 27542599

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Project description:High environmental temperature has strong adverse effects on poultry production, welfare, and sustainability and, thereby, constitutes one of the most challenging stressors. Although colossal information has been published on the effects of heat stress on poultry productivity and gut health, the fundamemntal mechanisms associated with heat stress responses and intestinal barrier function are still not well defined. The aim of the present study was, therefore, to determine the effects of acute (2 h) heat stress on growth performance, gut integrity, and intestinal expression of heat shock and tight junction proteins in slow- (broilers of the 1950's, ACRB), moderate- (broilers of 1990's, 95RAN), rapid-(modern broilers, MRB) growing birds, and their ancestor wild jungle fowl (JF). Heat stress exposure significantly increased the core body temperature of 95RAN and MRB chickens by ~0.5-1°C, but not that of JF and ACRB compared to their counterparts maintained at thermoneutral conditions. Heat stress also depressed feed intake and increased serum fluorescein isothiocyanate-dextran (FITC-D) levels (P < 0.05) in modern broilers (95RAN and MRB) but not in JF and ACRB, indicating potential leaky gut syndrome. Molecular analyses showed that heat stress exposure significantly up regulated the duodenal expression of occludin (OCLN) and lipocalin (LCN2) in ACRB, zonula occludens (ZO-2), villin1 (VIL1), and calprotectin (CALPR) in 95 RAN, and only CALPR in MRB compared to their TN counterparts. In the jejunum however, heat stress down regulated the expression of PALS1-associated tight junction protein (PATJ) in ACRB, 95RAN, and MRB, and that of cadherin1 (CDH1) in MRB. In the ileum, heat stress significantly down regulated the expression of OCLN in 95 RAN, ZO-1 in MRB, gap junction protein alpha1 (GJA1) in JF, and VIL1 in ACRB compared to their TN counterparts. In summary, this is the first report, to our knowledge, showing that tight junction protein expression is environmental-, genotype-, and intestinal segment-dependent and identifying molecular signatures, such as CDH1, CALPR, and ZO-1, potentially involved in leaky gut syndrome-induced by heat stress in MRB.

Dataset Information

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.

Publications

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.

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