Preprint Article Version 1 This version is not peer-reviewed

Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Version 1 : Received: 3 November 2018 / Approved: 5 November 2018 / Online: 5 November 2018 (11:33:17 CET)

A peer-reviewed article of this Preprint also exists.

Clark, F.E.; Conte, M.A.; Kocher, T.D. Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes. Genes 2018, 9, 610. Clark, F.E.; Conte, M.A.; Kocher, T.D. Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes. Genes 2018, 9, 610.

Journal reference: Genes 2018, 9, 610
DOI: 10.3390/genes9120610

Abstract

B chromosomes (Bs) were discovered a century ago, and since then most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function and evolution of B chromosomes remain unanswered. Here we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with and without B chromosomes. We examine the efficiency of this method, and compare results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets are identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified candidate genes located on the B chromosome which may regulate the segregation and maintenance of the B chromosome.

Subject Areas

supernumerary chromosomes; B chromosomes; next-generation sequencing, coverage ratio analysis

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