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

BMC Genomics

Research Article

Benoît Piégu¹  Florian Guillou¹  Sébastien Guizard¹  Yves Bigot¹  Peter Arensburger² 

[1] Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380, Nouzilly, France;Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380, Nouzilly, France;Biological Sciences Department, California State Polytechnic University, 91768, Pomona, CA, USA;

关键词: Satellite DNA;    Transposable elements;    Bioinformatics;    Benchmarking;    Repeat;   

DOI  :  10.1186/s12864-016-3015-5

 received in 2016-03-28, accepted in 2016-08-12,  发布年份 2016

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2016