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Open AccessArticle

Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata

Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil
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Genes 2018, 9(6), 269; https://doi.org/10.3390/genes9060269
Received: 17 March 2018 / Revised: 16 May 2018 / Accepted: 17 May 2018 / Published: 23 May 2018
(This article belongs to the Special Issue Evolution, Composition and Regulation of Supernumerary B Chromosomes)
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome. View Full-Text
Keywords: repetitive elements; RNA-Seq; genomics; evolution; cytogenetics; supernumerary elements; extra chromosomes repetitive elements; RNA-Seq; genomics; evolution; cytogenetics; supernumerary elements; extra chromosomes
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Coan, R.L.B.; Martins, C. Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata. Genes 2018, 9, 269.

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