Origin and evolution of B chromosomes in the cichlid fish Astatotilapia latifasciata based on integrated genomic analyses.
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.
Department of Morphology, Biosciences Institute, São Paulo State University, São Paulo, Brazil.
Guilherme T
GT
Valente
Department of Biology, University of Maryland, College Park.
Matthew A
MA
Conte
Department of Morphology, Biosciences Institute, São Paulo State University, São Paulo, Brazil.
Bruno E A
BE
Fantinatti
Department of Biology, Biosciences Institute, São Paulo State University, São Paulo, Brazil.
Diogo C
DC
Cabral-de-Mello
Department of Morphology, Biosciences Institute, São Paulo State University, São Paulo, Brazil.
Robson F
RF
Carvalho
Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Paraná, Brazil.
Marcelo R
MR
Vicari
Department of Biology, University of Maryland, College Park.
Thomas D
TD
Kocher
Department of Morphology, Biosciences Institute, São Paulo State University, São Paulo, Brazil cmartins@ibb.unesp.br cmartinsunesp@gmail.com.
Cesar
C
Martins
D000818:Animals; D002875:Chromosomes / Q000235:genetics*; D023681:Cichlids / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics*; D020440:Gene Duplication; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D059785:Karyotype; D008958:Models, Molecular; D017422:Sequence Analysis, DNA
D029941:Fish Proteins
chromosome evolution; genome evolution; next generation sequencing; supernumerary chromosome