Characterization and genetic variations of satellite DNAs inAcrossocheilus paradoxus(Günther, 1868) (Cyprinidae) indicate population expansion

Abstract

A Hin dIII repetitive DNA family from Acrossocheilus paradoxus, a cyprinid fish endemic to Taiwan, was isolated and identified as a tandem arrangement of satellites in the genomic DNA. Cross-hybridization revealed similar patterns across fish genera and two families and suggested that this repetitive DNA is a conserved satellite sequence in fish. Forty-five monomeric repeat units of the repetitive DNA were cloned and sequenced, and found to be approximately 210 base pairs long and to have an average base composition of 52Á8% AþT. Alignment analysis by examining 45 cloned repeat DNA strands from 22 individuals from nine different streams suggested that this repetitive DNA is highly polymorphic. The variability of sequences was mainly attributable to point mutations within the sequences. Genetic distances in all repeated DNAs ranged from 0 to 0Á129 (average, 0Á06). The high levels of genotype diversity and low levels of nucleotide diversity in satellites suggest population expansion of A. paradoxus. #

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…This is thought to occur either by genetic isolation between populations or by the propagation of new mutational variants across neighboring populations through molecular biological processes such as biased gene conversion (Elder & Turner, ). Similar results were recorded in A. paradoxus (Tseng et al., ) for the satellite sequence to which our Labeobarbus satellite matches. In agreement with this, we analyzed a set of Hin dIII satellite SNPs independently to our neutral SNPs and found similar results of genetic structure between the populations identified in this study (data not shown).…”

“…Cyprinid genomes include extensive repetitive regions (Henkel et al, 2012) such as the HindIII satellite (Datta, Dutta, & Mandal, 1988;Tseng, Chiang, & Wang, 2008), which is prevalent in our dataset at a frequency of 4.26% prior to filtering, with 7.47% of the loci in the final dataset potentially affiliated with this satellite. The prevalence of this satellite in our data exceeds that of all satellites across the C. carpio genome (2.46%) (Xu et al, 2011).…”