Approximately 15% of eukaryotes contain supernumerary B chromosomes. When present, B chromosomes frequently represent as much as 5% of the genome. Despite thousands of reports describing the distribution of supernumeraries in various taxa, a comprehensive theory for the origin, maintenance, and evolution of B chromosomes has not emerged. Here, we sequence the complete genomes of individual cichlid fish (Astatotilapia latifasciata) with and without B chromosomes, as well as microdissected B chromosomes, to identify DNA sequences on the B. B sequences were further analyzed through quantitative polymerase chain reaction and in situ hybridization. We find that the B chromosome contains thousands of sequences duplicated from essentially every chromosome in the ancestral karyotype. Although most genes on the B chromosome are fragmented, a few are largely intact, and we detect evidence that at least three of them are transcriptionally active. We propose a model in which the B chromosome originated early in the evolutionary history of Lake Victoria cichlids from a small fragment of one autosome. DNA sequences originating from several autosomes, including protein-coding genes and transposable elements, subsequently inserted into this proto-B. We propose that intact B chromosome genes involved with microtubule organization, kinetochore structure, recombination and progression through the cell cycle may play a role in driving the transmission of the B chromosome. Furthermore, our work suggests that karyotyping is an essential step prior to genome sequencing to avoid problems in genome assembly and analytical biases created by the presence of high copy number sequences on the B chromosome.

The heterochromatin composition and loca- tion in the genome of the fish Astyanax janeiroensis was investigated using Chromomycin A3 and DAPI fluorochromes and fluorescence in situ hybridization (FISH) with 18S rDNA and As51 satellite DNA probes, respectively. Distinct repetitive DNA classes were found, namely: (1) C-positive centromeric/telomeric heterochromatin, (2) NOR-associated GC-rich heterochromatin (18S+/GC+) and (3) As51+/18S+ heterochromatin colocalized on 14 distinct heterochromatic domains with attenuated fluorescence of DAPI staining (As51+/18S+/DAPI attenuated signal).Besides these fourteen associated repetitive DNAs, another eight sites with only 18S rDNA were also found, comprising altogether 22 18S rDNA sites in the genome of the species under study. Up to seven 18S rDNA sites were found to be active, i.e., were characterized as positive after silver staining (Ag-NORs). It was noteworthy that in all As51+/18S+ domains the 18S rDNA were not found to be active sites due to the silencing of these genes when associated with the As51 satellite DNA in the same heterochromatic domain. The dispersion of the As51 sites in the genome of the species is hypothesized to probably originate from a transposable element. Several chromosomal and karyotype markers are similar between A. janeiroensis and A. scabripinnis, indicating a close relationship between these species.