Abstract
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.
Highlights
B chromosomes (Bs) are supernumerary elements in addition to autosomal (A) chromosomes and have been observed in several species of animals, plants, and fungi
long interspersed nuclear element (LINE) had both higher copy number and more bases masked on the genome
short interspersed nuclear element (SINE) are present in higher number than long terminal repeat (LTR), but LTRs have more bases masked on the genome, probably due to their larger size
Summary
B chromosomes (Bs) are supernumerary elements in addition to autosomal (A) chromosomes and have been observed in several species of animals, plants, and fungi. B chromosomes are usually heterochromatic due to the abundance of repetitive elements in their composition [5]. Regardless of the predominance of repetitive content on Bs, they can carry genes with different levels of integrity, including fully transcribed copies. Gene copies found on B chromosomes can modulate the gene expression of A-complement genes and even influence metabolic pathways [6,7,8]. B chromosomes usually consist of a mosaic of sequences from the A complement; B origin is generally linked to genomic instability in the A chromosomes and involves the formation of a proto-B and later expansion of repetitive elements [9,10,11]. Repetitive elements, including transposable elements (TEs—DNA transposons and retrotransposons) [12,13,14,15], represent a large portion of most
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